Invalid argument: --no-solvation Usage: /nfs/home/rstein/zzz.github/DOCK/ligand/generate/build_database_ligand.sh [OPTIONS] Options: -h, --help - Display this message and exit -H, --pH - A quoted, space separated list of pH levels to build tautomers/protomers at -s, --single - Build a single db/db2 file instead of separate files for each protomer -n, --name - Override database name -d, --dir - Working directory -c, --covalent - Build a covalent library instead of standard -3, --3d - Use provided 3D structures (implies --pre-tautomerized) --no-limit-confs-by-hydrogens - Don't limit # conformations by # rotatable hydrogens --pre-tautomerized - Treat input file as pre-generated tautomers --permissive-taut-prot - Use lower tautomer and protomer cutoffs --no-conformations - Skip generating multiple rigid fragment conformations --no-db - Skip building db files --no-db2 - Skip building db2 files --no-solvation - Don't save solvation files --no-mol2 - Don't save mol2 files --save-table - Save the full protomer table --bad-charges - List of bad protonation patterns to exclude --debug - Extra debugging output Overrideable Sub-programs: TAUOMERIZE_PROTONATE_EXE - Generate (multiple) tautomerized and protonated variants of the input substances at a pH level PROTOMER_COALESE_EXE - Filter and merge protomers over pH levels PROTOMER_STEREOCENTERS_EXE - Expand any new stereocenters from protonation EMBED_PROTOMERS_3D_EXE - Create 3D mol2 files for each protomer (names should JUST be the line number of the protomer without any extension) PREPARE_NAME_EXE - Write the name.txt file to build a db2 file with SOLVATION_EXE - Calculation solvation for a given mol2 file GENERATE_CONFORMATIONS_EXE - Generate heirarchy conformations GENERATE_RIGID_FRAGMENT_CONFORMATIONS_EXE - Generate standard heirarchy conformations GENERATE_COVALENT_CONFORMATIONS_EXE - Generate covalent heirarchy conformations BUILD_DB2_EXE - Generate a db2 file from conformations BUILD_DB_EXE - Genearte a db file from conformations STORE_PROTOMERS is not set! Will keep all results to finished directory mkdir: created directory `/scratch/stefan/7770410/working' mkdir: created directory `/scratch/stefan/7770410/working/protonate' Storing results in /scratch/stefan/7770410/finished Working in /scratch/stefan/7770410/working /scratch/stefan/7770410/working /scratch/stefan/7770410 /scratch/stefan/7770410/working/protonate /scratch/stefan/7770410/working /scratch/stefan/7770410 Precomputing protomers for all compounds (pH: 7.4) rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: `/nfs/home/stefan/.install4j_new' and `/nfs/home/stefan/.install4j' are the same file mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory ph 7.4: 2010 protomers created Coalesing and merging protomers 1998 protomers generated for 1000 compounds Checking for new stereocenters and expanding 2020 protomers after new stereo-center expansion /scratch/stefan/7770410/working /scratch/stefan/7770410 Bulk generating 3D conformations all protomers in /scratch/stefan/7770410/working/3D mkdir: created directory `/scratch/stefan/7770410/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7770410/working/protonate/xaaaata-protomers-expanded.ism /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' 2021 3D conformations generated for 1000 compounds Building REAL300020113202 mkdir: created directory `/scratch/stefan/7770410/working/building' mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113202' /scratch/stefan/7770410/working/building/REAL300020113202 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113202 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113202/0 /scratch/stefan/7770410/working/building/REAL300020113202 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1 `/scratch/stefan/7770410/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020113202.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113202 none CC1=CC=CC(C(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 23, 31, 31, 12, 6, 12, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 32, 45, 48, 48, 48, 48, 10, 10, 1, 31, 31, 31, 31, 23, 31, 31, 12, 12, 12, 12, 6, 1, 1, 1, 1, 10, 32, 32, 45, 45, 1, 1, 31] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50]) total number of confs: 278 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113202 none CC1=CC=CC(C(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 92, 102, 102, 53, 30, 53, 30, 30, 10, 10, 10, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 10, 102, 102, 102, 102, 92, 102, 102, 53, 53, 53, 53, 30, 10, 10, 10, 10, 1, 7, 7, 9, 9, 10, 10, 102] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 341 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113202 none CC1=CC=CC(C(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 11, 11, 11, 31, 31, 31, 102, 102, 102, 167, 201, 201, 201, 201, 201, 102, 102, 31, 1, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5, 11, 31, 31, 31, 31, 102, 167, 167, 201, 201, 31, 31, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 50, 33, 27, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 737 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113202 none CC1=CC=CC(C(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 116, 84, 116, 84, 84, 48, 48, 48, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 48, 201, 201, 201, 201, 201, 201, 201, 116, 116, 116, 116, 84, 48, 48, 48, 48, 11, 6, 6, 4, 4, 48, 48, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 584 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113202 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113202/1 /scratch/stefan/7770410/working/building/REAL300020113202 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/2 `/scratch/stefan/7770410/working/3D/2' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020113202.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113202 none CC1=CC=CC(C(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 23, 32, 32, 12, 6, 12, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 32, 45, 48, 48, 48, 48, 10, 10, 1, 32, 32, 32, 32, 23, 32, 32, 12, 12, 12, 12, 6, 1, 1, 1, 1, 10, 32, 32, 45, 45, 1, 1, 32] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50]) total number of confs: 282 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113202 none CC1=CC=CC(C(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 93, 103, 103, 53, 30, 53, 30, 30, 10, 10, 10, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 10, 103, 103, 103, 103, 93, 103, 103, 53, 53, 53, 53, 30, 10, 10, 10, 10, 1, 7, 7, 9, 9, 10, 10, 103] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 343 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113202 none CC1=CC=CC(C(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 11, 11, 11, 32, 32, 32, 103, 103, 103, 167, 201, 201, 201, 201, 201, 103, 103, 32, 1, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5, 11, 32, 32, 32, 32, 103, 167, 167, 201, 201, 32, 32, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 50, 33, 27, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 730 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113202 none CC1=CC=CC(C(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 116, 85, 116, 85, 85, 49, 49, 49, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 49, 201, 201, 201, 201, 201, 201, 201, 116, 116, 116, 116, 85, 49, 49, 49, 49, 12, 6, 6, 4, 4, 49, 49, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 579 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113202 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113202 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `/scratch/stefan/7770410/finished' Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113202/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113202/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113202 Building REAL300020113203 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113203' /scratch/stefan/7770410/working/building/REAL300020113203 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113203 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113203/0 /scratch/stefan/7770410/working/building/REAL300020113203 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/3 `/scratch/stefan/7770410/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C(C)C)=N1) `REAL300020113203.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113203 none CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [55, 26, 26, 26, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 25, 33, 41, 41, 41, 41, 7, 7, 1, 26, 26, 26, 26, 26, 55, 55, 55, 55, 55, 26, 6, 1, 1, 1, 1, 7, 25, 25, 33, 33, 1, 1, 26, 26, 26, 26, 26, 26, 26] 180 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 45, 46, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 322 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113203 none CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [110, 62, 62, 62, 22, 22, 22, 7, 7, 7, 1, 1, 1, 1, 1, 8, 10, 14, 14, 14, 14, 1, 1, 7, 62, 62, 62, 62, 62, 110, 110, 110, 110, 110, 62, 22, 7, 7, 7, 7, 1, 8, 8, 10, 10, 7, 7, 62, 62, 62, 62, 62, 62, 62] 180 rigid atoms, others: [40, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 407 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113203 none CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 1, 1, 1, 1, 8, 8, 8, 26, 26, 26, 62, 62, 62, 109, 130, 138, 138, 138, 138, 62, 62, 26, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 8, 26, 26, 26, 26, 62, 109, 109, 130, 130, 26, 26, 1, 2, 2, 2, 2, 2, 2] 180 rigid atoms, others: [1, 2, 3, 4, 5, 34, 47, 24, 25, 26, 27, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 497 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113203 none CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [181, 140, 140, 140, 85, 85, 85, 48, 48, 48, 22, 22, 22, 7, 4, 1, 1, 1, 1, 1, 1, 22, 22, 48, 140, 140, 140, 140, 140, 181, 181, 181, 181, 181, 140, 85, 48, 48, 48, 48, 22, 7, 7, 4, 4, 48, 48, 140, 140, 140, 140, 140, 140, 140] 181 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 579 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113203 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113203/1 /scratch/stefan/7770410/working/building/REAL300020113203 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/4 `/scratch/stefan/7770410/working/3D/4' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C(C)C)=N1) `REAL300020113203.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113203/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113203 none CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [57, 26, 26, 26, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 24, 32, 41, 41, 41, 41, 7, 7, 1, 26, 26, 26, 26, 26, 57, 57, 57, 57, 57, 26, 6, 1, 1, 1, 1, 7, 24, 24, 32, 32, 1, 1, 26, 26, 26, 26, 26, 26, 26] 177 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 45, 46, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 327 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113203 none CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [109, 62, 62, 62, 22, 22, 22, 7, 7, 7, 1, 1, 1, 1, 1, 8, 10, 14, 14, 14, 14, 1, 1, 7, 62, 62, 62, 62, 62, 109, 109, 109, 109, 109, 62, 22, 7, 7, 7, 7, 1, 8, 8, 10, 10, 7, 7, 62, 62, 62, 62, 62, 62, 62] 177 rigid atoms, others: [40, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 401 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113203 none CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 1, 1, 1, 1, 8, 8, 8, 26, 26, 26, 62, 62, 62, 107, 127, 137, 137, 137, 137, 62, 62, 26, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 8, 26, 26, 26, 26, 62, 107, 107, 127, 127, 26, 26, 1, 2, 2, 2, 2, 2, 2] 177 rigid atoms, others: [1, 2, 3, 4, 5, 34, 47, 24, 25, 26, 27, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 489 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113203 none CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [177, 136, 136, 136, 83, 83, 83, 48, 48, 48, 22, 22, 22, 7, 4, 1, 1, 1, 1, 1, 1, 22, 22, 48, 136, 136, 136, 136, 136, 177, 177, 177, 177, 177, 136, 83, 48, 48, 48, 48, 22, 7, 7, 4, 4, 48, 48, 136, 136, 136, 136, 136, 136, 136] 177 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 568 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113203 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113203 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113203/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113203/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113203 Building REAL300020113204 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113204' /scratch/stefan/7770410/working/building/REAL300020113204 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113204 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113204/0 /scratch/stefan/7770410/working/building/REAL300020113204 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/5 `/scratch/stefan/7770410/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1C=C(Cl)C=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113204.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113204 none O=C(CN1C=C(Cl)C=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 16, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 29, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 10, 10, 10, 29, 43, 46, 46, 46, 46, 10, 10, 1, 29, 29, 40, 40, 6, 1, 1, 1, 1, 10, 29, 29, 43, 43, 1, 1] 201 rigid atoms, others: [32, 33, 34, 40, 9, 10, 11, 12, 13, 41, 25, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) total number of confs: 297 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113204 none O=C(CN1C=C(Cl)C=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 16, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 101, 109, 109, 109, 109, 109, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 10, 101, 101, 109, 109, 32, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10] 201 rigid atoms, others: [35, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 403 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113204 none O=C(CN1C=C(Cl)C=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 16, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 5, 1, 1, 1, 1, 1, 1, 1, 17, 17, 40, 40, 40, 109, 109, 109, 169, 201, 201, 201, 201, 201, 109, 109, 40, 5, 5, 1, 1, 17, 40, 40, 40, 40, 109, 169, 169, 201, 201, 40, 40] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 28, 29] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 706 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113204 none O=C(CN1C=C(Cl)C=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 16, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 201, 201, 201, 201, 201, 201, 46, 46, 46, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 46, 201, 201, 201, 201, 107, 46, 46, 46, 46, 9, 5, 5, 3, 3, 46, 46] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 736 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113204 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113204/1 /scratch/stefan/7770410/working/building/REAL300020113204 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/6 `/scratch/stefan/7770410/working/3D/6' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1C=C(Cl)C=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113204.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113204 none O=C(CN1C=C(Cl)C=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 16, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 29, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 10, 10, 10, 29, 43, 46, 46, 46, 46, 10, 10, 1, 29, 29, 39, 39, 6, 1, 1, 1, 1, 10, 29, 29, 43, 43, 1, 1] 201 rigid atoms, others: [32, 33, 34, 40, 9, 10, 11, 12, 13, 41, 25, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) total number of confs: 295 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113204 none O=C(CN1C=C(Cl)C=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 16, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 103, 110, 110, 110, 110, 110, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 10, 103, 103, 110, 110, 32, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10] 201 rigid atoms, others: [35, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 410 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113204 none O=C(CN1C=C(Cl)C=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 16, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 5, 1, 1, 1, 1, 1, 1, 1, 17, 17, 39, 39, 39, 110, 110, 110, 169, 201, 201, 201, 201, 201, 110, 110, 39, 5, 5, 1, 1, 17, 39, 39, 39, 39, 110, 169, 169, 201, 201, 39, 39] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 28, 29] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 699 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113204 none O=C(CN1C=C(Cl)C=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 16, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 201, 201, 201, 201, 201, 201, 47, 47, 47, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 47, 201, 201, 201, 201, 107, 47, 47, 47, 47, 10, 5, 5, 3, 3, 47, 47] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 736 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113204 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113204 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113204/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113204/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113204 Building REAL300020113205 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113205' /scratch/stefan/7770410/working/building/REAL300020113205 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113205 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113205/0 /scratch/stefan/7770410/working/building/REAL300020113205 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/7 `/scratch/stefan/7770410/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)NCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113205.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113205 none CN(C)S(=O)(=O)NCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 65, 74, 74, 59, 20, 20, 20, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 7, 74, 74, 74, 74, 74, 74, 65, 59, 59, 20, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 342 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113205 none CN(C)S(=O)(=O)NCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 192, 105, 105, 105, 56, 56, 56, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 56, 201, 201, 201, 201, 201, 201, 201, 192, 192, 105, 56, 56, 56, 56, 15, 6, 6, 4, 4, 56, 56] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 726 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113205 none CN(C)S(=O)(=O)NCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 24, 27, 27, 20, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 38, 48, 56, 56, 56, 56, 7, 7, 1, 27, 27, 27, 27, 27, 27, 24, 20, 20, 6, 1, 1, 1, 1, 7, 38, 38, 48, 48, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113205 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113205/1 /scratch/stefan/7770410/working/building/REAL300020113205 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/8 `/scratch/stefan/7770410/working/3D/8' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)NCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113205.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113205/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113205 none CN(C)S(=O)(=O)NCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 66, 75, 75, 60, 20, 20, 20, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 7, 75, 75, 75, 75, 75, 75, 66, 60, 60, 20, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 343 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113205 none CN(C)S(=O)(=O)NCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 192, 106, 106, 106, 57, 57, 57, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 57, 201, 201, 201, 201, 201, 201, 201, 192, 192, 106, 57, 57, 57, 57, 15, 6, 6, 4, 4, 57, 57] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 722 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113205 none CN(C)S(=O)(=O)NCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 24, 27, 27, 20, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 37, 47, 56, 56, 56, 56, 7, 7, 1, 27, 27, 27, 27, 27, 27, 24, 20, 20, 6, 1, 1, 1, 1, 7, 37, 37, 47, 47, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113205 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113205 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113205/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113205/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113205 Building REAL300020113206 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113206' /scratch/stefan/7770410/working/building/REAL300020113206 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113206 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113206/0 /scratch/stefan/7770410/working/building/REAL300020113206 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/9 `/scratch/stefan/7770410/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1) `REAL300020113206.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113206 none CCC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 28, 13, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 19, 30, 30, 30, 30, 30, 7, 7, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 13, 13, 5, 1, 1, 1, 1, 7, 19, 19, 30, 30, 1, 1, 28, 28] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50]) total number of confs: 200 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113206 none CCC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 114, 116, 116, 57, 22, 22, 22, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 116, 116, 116, 116, 116, 116, 116, 116, 116, 57, 57, 22, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 116, 116] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 351 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113206 none CCC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 28, 28, 28, 116, 116, 116, 159, 201, 201, 201, 201, 201, 116, 116, 28, 1, 1, 2, 2, 2, 2, 2, 1, 1, 6, 6, 13, 28, 28, 28, 28, 116, 159, 159, 201, 201, 28, 28, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 34, 49, 50, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 677 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113206 none CCC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 198, 201, 201, 101, 51, 51, 51, 30, 30, 30, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 30, 201, 201, 201, 201, 201, 201, 201, 201, 201, 101, 101, 51, 30, 30, 30, 30, 7, 4, 4, 2, 2, 30, 30, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 583 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113206 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113206/1 /scratch/stefan/7770410/working/building/REAL300020113206 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/10 `/scratch/stefan/7770410/working/3D/10' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1) `REAL300020113206.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113206 none CCC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 28, 13, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 19, 30, 30, 30, 30, 30, 7, 7, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 13, 13, 5, 1, 1, 1, 1, 7, 19, 19, 30, 30, 1, 1, 28, 28] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50]) total number of confs: 200 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113206 none CCC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 114, 116, 116, 57, 22, 22, 22, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 116, 116, 116, 116, 116, 116, 116, 116, 116, 57, 57, 22, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 116, 116] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 351 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113206 none CCC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 28, 28, 28, 116, 116, 116, 159, 201, 201, 201, 201, 201, 116, 116, 28, 1, 1, 2, 2, 2, 2, 2, 1, 1, 6, 6, 13, 28, 28, 28, 28, 116, 159, 159, 201, 201, 28, 28, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 34, 49, 50, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 677 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113206 none CCC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 198, 201, 201, 101, 52, 52, 52, 30, 30, 30, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 30, 201, 201, 201, 201, 201, 201, 201, 201, 201, 101, 101, 52, 30, 30, 30, 30, 7, 4, 4, 2, 2, 30, 30, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 584 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113206 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113206 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113206/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113206/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113206 Building REAL300020113207 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113207' /scratch/stefan/7770410/working/building/REAL300020113207 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113207 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113207/0 /scratch/stefan/7770410/working/building/REAL300020113207 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/11 `/scratch/stefan/7770410/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1=O) `REAL300020113207.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113207 none CCCN1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 41, 18, 18, 18, 5, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 26, 39, 39, 39, 39, 39, 10, 10, 1, 18, 18, 18, 45, 45, 45, 45, 45, 41, 41, 18, 18, 18, 5, 1, 1, 1, 1, 10, 26, 26, 39, 39, 1, 1, 18, 18] 201 rigid atoms, others: [49, 39, 8, 9, 10, 11, 12, 48, 40, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50, 51]) total number of confs: 334 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113207 none CCCN1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 128, 72, 72, 72, 26, 26, 26, 10, 10, 10, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 10, 72, 72, 72, 133, 133, 133, 133, 133, 128, 128, 72, 72, 72, 26, 10, 10, 10, 10, 1, 5, 5, 7, 7, 10, 10, 72, 72] 201 rigid atoms, others: [11, 43, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 545 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113207 none CCCN1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 1, 1, 1, 1, 1, 8, 8, 8, 18, 18, 18, 72, 72, 72, 104, 131, 131, 131, 131, 131, 72, 72, 18, 1, 1, 1, 6, 6, 6, 5, 5, 4, 4, 1, 1, 1, 8, 18, 18, 18, 18, 72, 104, 104, 131, 131, 18, 18, 1, 1] 201 rigid atoms, others: [51, 2, 35, 4, 5, 6, 50, 3, 25, 36, 26, 27, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 457 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113207 none CCCN1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 138, 138, 138, 75, 75, 75, 37, 37, 37, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 37, 138, 138, 138, 201, 201, 201, 201, 201, 201, 201, 138, 138, 138, 75, 37, 37, 37, 37, 7, 4, 4, 2, 2, 37, 37, 138, 138] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 778 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113207 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113207/1 /scratch/stefan/7770410/working/building/REAL300020113207 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/12 `/scratch/stefan/7770410/working/3D/12' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1=O) `REAL300020113207.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113207 none CCCN1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 41, 18, 18, 18, 5, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 26, 39, 39, 39, 39, 39, 10, 10, 1, 18, 18, 18, 45, 45, 45, 45, 45, 41, 41, 18, 18, 18, 5, 1, 1, 1, 1, 10, 26, 26, 39, 39, 1, 1, 18, 18] 201 rigid atoms, others: [49, 39, 8, 9, 10, 11, 12, 48, 40, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50, 51]) total number of confs: 334 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113207 none CCCN1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 128, 72, 72, 72, 26, 26, 26, 10, 10, 10, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 10, 72, 72, 72, 133, 133, 133, 133, 133, 128, 128, 72, 72, 72, 26, 10, 10, 10, 10, 1, 5, 5, 7, 7, 10, 10, 72, 72] 201 rigid atoms, others: [11, 43, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 545 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113207 none CCCN1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 1, 1, 1, 1, 1, 8, 8, 8, 18, 18, 18, 72, 72, 72, 104, 130, 130, 130, 130, 130, 72, 72, 18, 1, 1, 1, 6, 6, 6, 5, 5, 4, 4, 1, 1, 1, 8, 18, 18, 18, 18, 72, 104, 104, 130, 130, 18, 18, 1, 1] 201 rigid atoms, others: [51, 2, 35, 4, 5, 6, 50, 3, 25, 36, 26, 27, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 451 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113207 none CCCN1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 138, 138, 138, 75, 75, 75, 37, 37, 37, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 37, 138, 138, 138, 201, 201, 201, 201, 201, 201, 201, 138, 138, 138, 75, 37, 37, 37, 37, 7, 4, 4, 2, 2, 37, 37, 138, 138] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 778 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113207 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113207 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113207/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113207/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113207 Building REAL300020113208 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113208' /scratch/stefan/7770410/working/building/REAL300020113208 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113208 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113208/0 /scratch/stefan/7770410/working/building/REAL300020113208 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/13 `/scratch/stefan/7770410/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)N1C=CN=C1) `REAL300020113208.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113208 none CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)N1C=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 61, 18, 18, 18, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 79, 131, 131, 131, 131, 79, 79, 79, 79, 61, 61, 18, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8, 131, 131, 131] 201 rigid atoms, others: [38, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 453 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113208 none CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)N1C=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 120, 54, 54, 54, 35, 35, 35, 8, 8, 8, 5, 3, 1, 1, 1, 1, 1, 1, 8, 8, 35, 133, 201, 201, 201, 201, 133, 133, 133, 133, 120, 120, 54, 35, 35, 35, 35, 8, 5, 5, 3, 3, 35, 35, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 677 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113208 none CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)N1C=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 18, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 20, 32, 32, 32, 32, 32, 8, 8, 1, 24, 41, 41, 41, 41, 24, 24, 24, 24, 18, 18, 5, 1, 1, 1, 1, 8, 20, 20, 32, 32, 1, 1, 41, 41, 41] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 43, 44, 21, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113208 none CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)N1C=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 7, 22, 22, 22, 41, 41, 41, 131, 131, 131, 170, 201, 201, 201, 201, 201, 131, 131, 41, 1, 1, 1, 1, 1, 2, 2, 2, 2, 7, 7, 22, 41, 41, 41, 41, 131, 170, 170, 201, 201, 41, 41, 1, 1, 1] 201 rigid atoms, others: [1, 45, 46, 47, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 640 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113208 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113208/1 /scratch/stefan/7770410/working/building/REAL300020113208 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/14 `/scratch/stefan/7770410/working/3D/14' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)N1C=CN=C1) `REAL300020113208.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113208/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113208 none CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)N1C=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 61, 18, 18, 18, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 8, 8, 8, 8, 1, 1, 8, 80, 129, 129, 129, 129, 80, 80, 80, 80, 61, 61, 18, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8, 129, 129, 129] 201 rigid atoms, others: [38, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 455 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113208 none CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)N1C=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [132, 120, 54, 54, 54, 35, 35, 35, 8, 8, 8, 5, 3, 1, 1, 1, 1, 1, 1, 8, 8, 35, 132, 201, 201, 201, 201, 132, 132, 132, 132, 120, 120, 54, 35, 35, 35, 35, 8, 5, 5, 3, 3, 35, 35, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 673 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113208 none CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)N1C=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 18, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 20, 32, 33, 33, 33, 33, 8, 8, 1, 24, 41, 41, 41, 41, 24, 24, 24, 24, 18, 18, 5, 1, 1, 1, 1, 8, 20, 20, 32, 32, 1, 1, 41, 41, 41] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 43, 44, 21, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113208 none CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)N1C=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 7, 22, 22, 22, 41, 41, 41, 129, 129, 129, 170, 201, 201, 201, 201, 201, 129, 129, 41, 1, 1, 1, 1, 1, 2, 2, 2, 2, 7, 7, 22, 41, 41, 41, 41, 129, 170, 170, 201, 201, 41, 41, 1, 1, 1] 201 rigid atoms, others: [1, 45, 46, 47, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 650 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113208 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113208 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113208/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113208/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113208 Building REAL300020113209 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113209' /scratch/stefan/7770410/working/building/REAL300020113209 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113209 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113209/0 /scratch/stefan/7770410/working/building/REAL300020113209 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/15 `/scratch/stefan/7770410/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=N1) `REAL300020113209.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113209 none CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 14, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 36, 51, 60, 60, 60, 60, 11, 11, 1, 14, 14, 14, 35, 35, 35, 35, 35, 14, 6, 1, 1, 1, 1, 11, 36, 36, 51, 51, 1, 1, 14, 14, 14] 201 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 339 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113209 none CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 72, 72, 72, 40, 40, 40, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 72, 72, 72, 117, 117, 117, 117, 117, 72, 40, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 72, 72, 72] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 423 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113209 none CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 72, 72, 72, 124, 160, 166, 166, 166, 166, 72, 72, 14, 1, 1, 1, 5, 5, 5, 5, 5, 1, 6, 14, 14, 14, 14, 72, 124, 124, 160, 160, 14, 14, 2, 2, 2] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 24, 25, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 599 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113209 none CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 166, 166, 166, 146, 146, 146, 61, 61, 61, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 61, 166, 166, 166, 201, 201, 201, 201, 201, 166, 146, 61, 61, 61, 61, 12, 6, 6, 4, 4, 61, 61, 166, 166, 166] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 648 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113209 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113209/1 /scratch/stefan/7770410/working/building/REAL300020113209 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/16 `/scratch/stefan/7770410/working/3D/16' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=N1) `REAL300020113209.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113209 none CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 14, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 38, 53, 63, 63, 63, 63, 11, 11, 1, 14, 14, 14, 35, 35, 35, 35, 35, 14, 6, 1, 1, 1, 1, 11, 38, 38, 53, 53, 1, 1, 14, 14, 14] 201 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 347 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113209 none CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 74, 74, 74, 40, 40, 40, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 74, 74, 74, 116, 116, 116, 116, 116, 74, 40, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 74, 74, 74] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 411 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113209 none CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 74, 74, 74, 127, 163, 170, 170, 170, 170, 74, 74, 14, 1, 1, 1, 5, 5, 5, 5, 5, 1, 6, 14, 14, 14, 14, 74, 127, 127, 163, 163, 14, 14, 2, 2, 2] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 24, 25, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 603 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113209 none CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 166, 166, 166, 146, 146, 146, 61, 61, 61, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 61, 166, 166, 166, 201, 201, 201, 201, 201, 166, 146, 61, 61, 61, 61, 12, 6, 6, 4, 4, 61, 61, 166, 166, 166] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 648 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113209 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113209 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113209/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113209/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113209 Building REAL300020113210 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113210' /scratch/stefan/7770410/working/building/REAL300020113210 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113210 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113210/0 /scratch/stefan/7770410/working/building/REAL300020113210 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/17 `/scratch/stefan/7770410/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1C) `REAL300020113210.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113210 none CC1=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 40, 58, 65, 65, 65, 65, 13, 13, 1, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 13, 40, 40, 58, 58, 1, 1, 11, 11, 11] 201 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 40, 41, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 269 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113210 none CC1=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 90, 49, 49, 49, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 90, 90, 90, 90, 90, 90, 49, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 90, 90, 90] 201 rigid atoms, others: [35, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 235 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113210 none CC1=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 90, 90, 90, 166, 201, 201, 201, 201, 201, 90, 90, 11, 1, 1, 1, 2, 2, 2, 3, 11, 11, 11, 11, 90, 166, 166, 201, 201, 11, 11, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 737 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113210 none CC1=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 149, 149, 149, 65, 65, 65, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 65, 201, 201, 201, 201, 201, 201, 149, 65, 65, 65, 65, 10, 6, 6, 4, 4, 65, 65, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 525 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113210 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113210/1 /scratch/stefan/7770410/working/building/REAL300020113210 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/18 `/scratch/stefan/7770410/working/3D/18' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1C) `REAL300020113210.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113210 none CC1=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 39, 57, 64, 64, 64, 64, 13, 13, 1, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 13, 39, 39, 57, 57, 1, 1, 11, 11, 11] 201 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 40, 41, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 266 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113210 none CC1=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 90, 49, 49, 49, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 90, 90, 90, 90, 90, 90, 49, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 90, 90, 90] 201 rigid atoms, others: [35, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 235 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113210 none CC1=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 90, 90, 90, 166, 201, 201, 201, 201, 201, 90, 90, 11, 1, 1, 1, 2, 2, 2, 3, 11, 11, 11, 11, 90, 166, 166, 201, 201, 11, 11, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 737 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113210 none CC1=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 149, 149, 149, 65, 65, 65, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 65, 201, 201, 201, 201, 201, 201, 149, 65, 65, 65, 65, 10, 6, 6, 4, 4, 65, 65, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 525 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113210 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113210 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113210/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113210/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113210 Building REAL300020113211 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113211' /scratch/stefan/7770410/working/building/REAL300020113211 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113211 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113211/0 /scratch/stefan/7770410/working/building/REAL300020113211 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/19 `/scratch/stefan/7770410/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=NN1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113211.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113211 none CC1=CC=NN1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 20, 6, 6, 6, 1, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 5, 5, 5, 4, 4, 1, 27, 27, 27, 27, 27, 20, 20, 6, 1, 1, 1, 1, 4, 5, 5, 5, 5, 1, 1] 32 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 94 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113211 none CC1=CC=NN1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 22, 9, 9, 9, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 4, 28, 28, 28, 28, 28, 22, 22, 9, 4, 4, 4, 4, 1, 4, 4, 4, 4, 4, 4] 32 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 104 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113211 none CC1=CC=NN1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 18, 18, 18, 27, 27, 27, 28, 28, 28, 32, 32, 32, 32, 32, 32, 28, 28, 27, 2, 2, 2, 1, 1, 6, 6, 18, 27, 27, 27, 27, 28, 32, 32, 32, 32, 27, 27] 32 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113211 none CC1=CC=NN1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 26, 14, 14, 14, 8, 8, 8, 6, 6, 6, 5, 2, 1, 1, 1, 1, 1, 1, 6, 6, 8, 32, 32, 32, 32, 32, 26, 26, 14, 8, 8, 8, 8, 6, 5, 5, 2, 2, 8, 8] 32 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 119 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113211 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113211/1 /scratch/stefan/7770410/working/building/REAL300020113211 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/20 `/scratch/stefan/7770410/working/3D/20' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=NN1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113211.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113211 none CC1=CC=NN1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 20, 6, 6, 6, 1, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 5, 5, 5, 4, 4, 1, 27, 27, 27, 27, 27, 20, 20, 6, 1, 1, 1, 1, 4, 5, 5, 5, 5, 1, 1] 32 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 94 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113211 none CC1=CC=NN1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 22, 9, 9, 9, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 4, 28, 28, 28, 28, 28, 22, 22, 9, 4, 4, 4, 4, 1, 4, 4, 4, 4, 4, 4] 32 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 104 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113211 none CC1=CC=NN1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 18, 18, 18, 27, 27, 27, 28, 28, 28, 32, 32, 32, 32, 32, 32, 28, 28, 27, 2, 2, 2, 1, 1, 6, 6, 18, 27, 27, 27, 27, 28, 32, 32, 32, 32, 27, 27] 32 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113211 none CC1=CC=NN1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 26, 14, 14, 14, 8, 8, 8, 6, 6, 6, 5, 2, 1, 1, 1, 1, 1, 1, 6, 6, 8, 32, 32, 32, 32, 32, 26, 26, 14, 8, 8, 8, 8, 6, 5, 5, 2, 2, 8, 8] 32 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 119 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113211 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113211 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113211/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113211/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113211 Building REAL300020113212 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113212' /scratch/stefan/7770410/working/building/REAL300020113212 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113212 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113212/0 /scratch/stefan/7770410/working/building/REAL300020113212 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/21 `/scratch/stefan/7770410/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NOC2=C1CCCCC2) `REAL300020113212.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113212 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NOC2=C1CCCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 12, 1, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 8, 8, 8, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 8, 29, 72, 72, 72, 72, 72, 72, 72, 72, 72, 29, 8, 8, 8, 8, 1, 9, 9, 11, 11, 8, 8, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 186 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113212 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NOC2=C1CCCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 12, 1, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [145, 145, 70, 70, 70, 19, 19, 19, 7, 4, 1, 1, 1, 1, 1, 1, 19, 19, 70, 145, 201, 201, 201, 201, 201, 201, 201, 201, 201, 145, 70, 70, 70, 70, 19, 7, 7, 4, 4, 70, 70, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 506 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113212 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NOC2=C1CCCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 12, 1, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 43, 53, 65, 65, 65, 65, 8, 8, 1, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 8, 43, 43, 53, 53, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 250 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113212 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NOC2=C1CCCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 12, 1, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 23, 23, 23, 72, 72, 72, 166, 201, 201, 201, 201, 201, 72, 72, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 23, 23, 23, 23, 72, 166, 166, 201, 201, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 767 number of broken/clashed sets: 201 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113212 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113212/1 /scratch/stefan/7770410/working/building/REAL300020113212 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/22 `/scratch/stefan/7770410/working/3D/22' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NOC2=C1CCCCC2) `REAL300020113212.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113212 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NOC2=C1CCCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 12, 1, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 8, 8, 8, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 8, 29, 72, 72, 72, 72, 72, 72, 72, 72, 72, 29, 8, 8, 8, 8, 1, 9, 9, 11, 11, 8, 8, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 186 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113212 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NOC2=C1CCCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 12, 1, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [145, 145, 71, 71, 71, 19, 19, 19, 7, 4, 1, 1, 1, 1, 1, 1, 19, 19, 71, 145, 201, 201, 201, 201, 201, 201, 201, 201, 201, 145, 71, 71, 71, 71, 19, 7, 7, 4, 4, 71, 71, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 504 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113212 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NOC2=C1CCCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 12, 1, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 43, 53, 65, 65, 65, 65, 8, 8, 1, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 8, 43, 43, 53, 53, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 250 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113212 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NOC2=C1CCCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 12, 1, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 23, 23, 23, 72, 72, 72, 166, 201, 201, 201, 201, 201, 72, 72, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 23, 23, 23, 23, 72, 166, 166, 201, 201, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 767 number of broken/clashed sets: 201 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113212 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113212 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113212/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113212/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113212 Building REAL300020113213 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113213' /scratch/stefan/7770410/working/building/REAL300020113213 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113213 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113213/0 /scratch/stefan/7770410/working/building/REAL300020113213 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/23 `/scratch/stefan/7770410/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1) `REAL300020113213.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113213 none CCCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 12, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 35, 35, 35, 35, 8, 8, 1, 12, 12, 27, 27, 27, 27, 27, 27, 27, 12, 5, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1, 12] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 45, 46, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47]) total number of confs: 236 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113213 none CCCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 52, 52, 52, 17, 17, 17, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 52, 52, 110, 110, 110, 110, 110, 110, 110, 52, 17, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 52] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 431 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113213 none CCCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 52, 52, 52, 92, 126, 126, 126, 126, 126, 52, 52, 12, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 5, 12, 12, 12, 12, 52, 92, 92, 126, 126, 12, 12, 1] 201 rigid atoms, others: [34, 3, 4, 5, 6, 2, 47, 25, 26] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 507 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113213 none CCCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 126, 126, 126, 54, 54, 54, 35, 35, 35, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 35, 126, 126, 201, 201, 201, 201, 201, 201, 201, 126, 54, 35, 35, 35, 35, 8, 4, 4, 2, 2, 35, 35, 126] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 716 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113213 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113213/1 /scratch/stefan/7770410/working/building/REAL300020113213 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/24 `/scratch/stefan/7770410/working/3D/24' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1) `REAL300020113213.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113213 none CCCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 12, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 35, 35, 35, 35, 8, 8, 1, 12, 12, 27, 27, 27, 27, 27, 27, 27, 12, 5, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1, 12] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 45, 46, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47]) total number of confs: 236 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113213 none CCCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 52, 52, 52, 17, 17, 17, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 52, 52, 109, 109, 109, 109, 109, 109, 109, 52, 17, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 52] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 425 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113213 none CCCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 52, 52, 52, 93, 127, 127, 127, 127, 127, 52, 52, 12, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 5, 12, 12, 12, 12, 52, 93, 93, 127, 127, 12, 12, 1] 201 rigid atoms, others: [34, 3, 4, 5, 6, 2, 47, 25, 26] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 510 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113213 none CCCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 127, 127, 127, 54, 54, 54, 35, 35, 35, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 35, 127, 127, 201, 201, 201, 201, 201, 201, 201, 127, 54, 35, 35, 35, 35, 8, 4, 4, 2, 2, 35, 35, 127] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 712 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113213 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113213 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113213/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113213/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113213 Building REAL300020113214 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113214' /scratch/stefan/7770410/working/building/REAL300020113214 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113214 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113214/0 /scratch/stefan/7770410/working/building/REAL300020113214 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/25 `/scratch/stefan/7770410/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CS1) `REAL300020113214.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113214 none CC1=NC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 28, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 32, 45, 48, 48, 48, 48, 9, 9, 1, 31, 31, 31, 31, 31, 28, 28, 6, 1, 1, 1, 1, 9, 32, 32, 45, 45, 1, 1, 31] 201 rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43]) total number of confs: 283 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113214 none CC1=NC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 99, 29, 29, 29, 9, 9, 9, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 9, 104, 104, 104, 104, 104, 99, 99, 29, 9, 9, 9, 9, 1, 8, 8, 10, 10, 9, 9, 104] 201 rigid atoms, others: [36, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 399 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113214 none CC1=NC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 11, 11, 11, 31, 31, 31, 104, 104, 104, 168, 201, 201, 201, 201, 201, 104, 104, 31, 1, 1, 2, 2, 2, 5, 5, 11, 31, 31, 31, 31, 104, 168, 168, 201, 201, 31, 31, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 43, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 704 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113214 none CC1=NC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 197, 98, 98, 98, 48, 48, 48, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 48, 201, 201, 201, 201, 201, 197, 197, 98, 48, 48, 48, 48, 12, 6, 6, 4, 4, 48, 48, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 746 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113214 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113214/1 /scratch/stefan/7770410/working/building/REAL300020113214 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/26 `/scratch/stefan/7770410/working/3D/26' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CS1) `REAL300020113214.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113214/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113214 none CC1=NC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 28, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 31, 44, 47, 47, 47, 47, 9, 9, 1, 31, 31, 31, 31, 31, 28, 28, 6, 1, 1, 1, 1, 9, 31, 31, 44, 44, 1, 1, 31] 201 rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43]) total number of confs: 280 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113214 none CC1=NC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 100, 30, 30, 30, 9, 9, 9, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 9, 104, 104, 104, 104, 104, 100, 100, 30, 9, 9, 9, 9, 1, 8, 8, 10, 10, 9, 9, 104] 201 rigid atoms, others: [36, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 399 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113214 none CC1=NC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 11, 11, 11, 31, 31, 31, 104, 104, 104, 168, 201, 201, 201, 201, 201, 104, 104, 31, 1, 1, 2, 2, 2, 5, 5, 11, 31, 31, 31, 31, 104, 168, 168, 201, 201, 31, 31, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 43, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 707 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113214 none CC1=NC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 197, 96, 96, 96, 47, 47, 47, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 47, 201, 201, 201, 201, 201, 197, 197, 96, 47, 47, 47, 47, 12, 6, 6, 4, 4, 47, 47, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 752 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113214 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113214 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113214/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113214/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113214 Building REAL300020113215 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113215' /scratch/stefan/7770410/working/building/REAL300020113215 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113215 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113215/0 /scratch/stefan/7770410/working/building/REAL300020113215 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/27 `/scratch/stefan/7770410/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CSC2=C1CCCC2) `REAL300020113215.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113215 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CSC2=C1CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 58, 129, 129, 129, 129, 129, 129, 129, 129, 58, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 129, 129, 129, 129, 129, 129, 129, 129, 129] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 285 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113215 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CSC2=C1CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [136, 136, 49, 49, 49, 10, 10, 10, 4, 2, 1, 1, 1, 1, 1, 1, 10, 10, 49, 136, 201, 201, 201, 201, 201, 201, 201, 201, 136, 49, 49, 49, 49, 10, 4, 4, 2, 2, 49, 49, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 471 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113215 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CSC2=C1CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 33, 47, 47, 47, 47, 47, 13, 13, 1, 6, 30, 30, 30, 30, 30, 30, 30, 30, 6, 1, 1, 1, 1, 13, 33, 33, 47, 47, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113215 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CSC2=C1CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 30, 30, 30, 129, 129, 129, 177, 201, 201, 201, 201, 201, 129, 129, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 30, 30, 30, 30, 129, 177, 177, 201, 201, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 591 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113215 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113215/1 /scratch/stefan/7770410/working/building/REAL300020113215 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/28 `/scratch/stefan/7770410/working/3D/28' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CSC2=C1CCCC2) `REAL300020113215.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113215 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CSC2=C1CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 58, 130, 130, 130, 130, 130, 130, 130, 130, 58, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 130, 130, 130, 130, 130, 130, 130, 130, 130] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 287 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113215 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CSC2=C1CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [136, 136, 47, 47, 47, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 47, 136, 201, 201, 201, 201, 201, 201, 201, 201, 136, 47, 47, 47, 47, 8, 4, 4, 2, 2, 47, 47, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 474 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113215 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CSC2=C1CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 33, 47, 47, 47, 47, 47, 13, 13, 1, 6, 30, 30, 30, 30, 30, 30, 30, 30, 6, 1, 1, 1, 1, 13, 33, 33, 47, 47, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113215 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CSC2=C1CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 30, 30, 30, 130, 130, 130, 177, 201, 201, 201, 201, 201, 130, 130, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 30, 30, 30, 30, 130, 177, 177, 201, 201, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 586 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113215 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113215 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113215/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113215/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113215 Building REAL300020113216 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113216' /scratch/stefan/7770410/working/building/REAL300020113216 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113216 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113216/0 /scratch/stefan/7770410/working/building/REAL300020113216 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/29 `/scratch/stefan/7770410/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCC1=CC=CS1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113216.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113216 none O=C(CCCC1=CC=CS1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 23, 29, 37, 51, 51, 51, 51, 1, 1, 1, 1, 1, 8, 8, 8, 18, 27, 27, 27, 27, 27, 8, 8, 1, 23, 23, 37, 37, 37, 37, 51, 51, 51, 5, 1, 1, 1, 1, 8, 18, 18, 27, 27, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 341 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113216 none O=C(CCCC1=CC=CS1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 84, 91, 121, 151, 151, 151, 151, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 84, 84, 121, 121, 121, 121, 151, 151, 151, 18, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 770 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113216 none O=C(CCCC1=CC=CS1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 7, 3, 3, 1, 1, 1, 1, 1, 1, 31, 31, 51, 51, 51, 151, 151, 151, 185, 201, 201, 201, 201, 201, 151, 151, 51, 7, 7, 3, 3, 3, 3, 1, 1, 1, 31, 51, 51, 51, 51, 151, 185, 185, 201, 201, 51, 51] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 573 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113216 none O=C(CCCC1=CC=CS1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 125, 125, 164, 201, 201, 201, 201, 26, 26, 26, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 26, 125, 125, 164, 164, 164, 164, 201, 201, 201, 36, 26, 26, 26, 26, 7, 4, 4, 2, 2, 26, 26] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 988 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113216 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113216/1 /scratch/stefan/7770410/working/building/REAL300020113216 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/30 `/scratch/stefan/7770410/working/3D/30' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCC1=CC=CS1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113216.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113216/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113216 none O=C(CCCC1=CC=CS1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 23, 29, 37, 51, 51, 51, 51, 1, 1, 1, 1, 1, 8, 8, 8, 18, 27, 27, 27, 27, 27, 8, 8, 1, 23, 23, 37, 37, 37, 37, 51, 51, 51, 5, 1, 1, 1, 1, 8, 18, 18, 27, 27, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 341 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113216 none O=C(CCCC1=CC=CS1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 84, 91, 121, 151, 151, 151, 151, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 84, 84, 121, 121, 121, 121, 151, 151, 151, 18, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 770 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113216 none O=C(CCCC1=CC=CS1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 7, 3, 3, 1, 1, 1, 1, 1, 1, 31, 31, 51, 51, 51, 151, 151, 151, 185, 201, 201, 201, 201, 201, 151, 151, 51, 7, 7, 3, 3, 3, 3, 1, 1, 1, 31, 51, 51, 51, 51, 151, 185, 185, 201, 201, 51, 51] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 573 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113216 none O=C(CCCC1=CC=CS1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 126, 127, 166, 201, 201, 201, 201, 26, 26, 26, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 26, 126, 126, 166, 166, 166, 166, 201, 201, 201, 37, 26, 26, 26, 26, 7, 4, 4, 2, 2, 26, 26] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 993 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113216 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113216 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113216/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113216/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113216 Building REAL300020113217 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113217' /scratch/stefan/7770410/working/building/REAL300020113217 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113217 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113217/0 /scratch/stefan/7770410/working/building/REAL300020113217 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/31 `/scratch/stefan/7770410/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C)C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1) `REAL300020113217.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113217 none CCC1=C(C)C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 13, 13, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 39, 55, 65, 65, 65, 65, 11, 11, 1, 13, 25, 25, 25, 25, 25, 13, 13, 13, 13, 6, 1, 1, 1, 1, 11, 39, 39, 55, 55, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 337 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113217 none CCC1=C(C)C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 56, 56, 56, 56, 56, 44, 44, 44, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 1, 1, 11, 56, 92, 92, 92, 92, 92, 56, 56, 56, 56, 44, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 391 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113217 none CCC1=C(C)C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 56, 56, 56, 105, 144, 147, 147, 147, 147, 56, 56, 13, 1, 2, 3, 3, 2, 2, 2, 2, 2, 1, 4, 13, 13, 13, 13, 56, 105, 105, 144, 144, 13, 13] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 35, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 580 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113217 none CCC1=C(C)C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 147, 147, 147, 147, 147, 139, 139, 139, 65, 65, 65, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 65, 147, 201, 201, 201, 201, 201, 147, 147, 147, 147, 139, 65, 65, 65, 65, 13, 6, 6, 4, 4, 65, 65] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 716 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113217 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113217/1 /scratch/stefan/7770410/working/building/REAL300020113217 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/32 `/scratch/stefan/7770410/working/3D/32' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C)C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1) `REAL300020113217.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113217 none CCC1=C(C)C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 14, 14, 14, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 39, 54, 64, 64, 64, 64, 11, 11, 1, 14, 26, 26, 26, 26, 26, 14, 14, 14, 14, 6, 1, 1, 1, 1, 11, 39, 39, 54, 54, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 332 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113217 none CCC1=C(C)C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 57, 57, 57, 57, 57, 44, 44, 44, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 1, 1, 11, 57, 93, 93, 93, 93, 93, 57, 57, 57, 57, 44, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 393 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113217 none CCC1=C(C)C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 57, 57, 57, 106, 144, 147, 147, 147, 147, 57, 57, 14, 1, 2, 3, 3, 2, 2, 2, 2, 2, 1, 4, 14, 14, 14, 14, 57, 106, 106, 144, 144, 14, 14] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 35, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 578 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113217 none CCC1=C(C)C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 147, 147, 147, 147, 147, 138, 138, 138, 64, 64, 64, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 64, 147, 201, 201, 201, 201, 201, 147, 147, 147, 147, 138, 64, 64, 64, 64, 13, 6, 6, 4, 4, 64, 64] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 716 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113217 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113217 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113217/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113217/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113217 Building REAL300020113218 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113218' /scratch/stefan/7770410/working/building/REAL300020113218 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113218 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113218/0 /scratch/stefan/7770410/working/building/REAL300020113218 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/33 `/scratch/stefan/7770410/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=NC=CN=C2C=C1) `REAL300020113218.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113218 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=NC=CN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 26, 72, 72, 72, 72, 72, 72, 72, 72, 72, 26, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 72, 72, 72, 72, 72] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 168 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113218 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=NC=CN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 47, 47, 47, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 47, 81, 201, 201, 201, 201, 201, 201, 201, 201, 201, 81, 47, 47, 47, 47, 10, 6, 6, 4, 4, 47, 47, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 415 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113218 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=NC=CN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 29, 43, 47, 47, 47, 47, 9, 9, 1, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 9, 29, 29, 43, 43, 1, 1, 13, 13, 13, 13, 13] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113218 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=NC=CN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 13, 13, 13, 72, 72, 72, 145, 201, 201, 201, 201, 201, 72, 72, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 13, 72, 145, 145, 201, 201, 13, 13, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 820 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113218 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113218/1 /scratch/stefan/7770410/working/building/REAL300020113218 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/34 `/scratch/stefan/7770410/working/3D/34' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=NC=CN=C2C=C1) `REAL300020113218.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113218 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=NC=CN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 26, 72, 72, 72, 72, 72, 72, 72, 72, 72, 26, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 72, 72, 72, 72, 72] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 168 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113218 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=NC=CN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 47, 47, 47, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 47, 81, 201, 201, 201, 201, 201, 201, 201, 201, 201, 81, 47, 47, 47, 47, 10, 6, 6, 4, 4, 47, 47, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 415 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113218 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=NC=CN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 29, 43, 47, 47, 47, 47, 9, 9, 1, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 9, 29, 29, 43, 43, 1, 1, 13, 13, 13, 13, 13] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113218 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=NC=CN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 13, 13, 13, 72, 72, 72, 145, 201, 201, 201, 201, 201, 72, 72, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 13, 72, 145, 145, 201, 201, 13, 13, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 820 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113218 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113218 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113218/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113218/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113218 Building REAL300020113219 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113219' /scratch/stefan/7770410/working/building/REAL300020113219 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113219 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113219/0 /scratch/stefan/7770410/working/building/REAL300020113219 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/35 `/scratch/stefan/7770410/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1C(=O)CNC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113219.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113219 none O=C(CN1C(=O)CNC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 6, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 28, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 8, 8, 8, 21, 33, 33, 33, 33, 33, 8, 8, 1, 28, 28, 41, 41, 41, 6, 1, 1, 1, 1, 8, 21, 21, 33, 33, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 43, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 251 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113219 none O=C(CN1C(=O)CNC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 6, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 90, 127, 127, 127, 127, 127, 127, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 90, 90, 127, 127, 127, 18, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [37, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 402 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113219 none O=C(CN1C(=O)CNC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 6, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 41, 41, 41, 127, 127, 127, 172, 201, 201, 201, 201, 201, 127, 127, 41, 2, 2, 1, 1, 1, 19, 41, 41, 41, 41, 127, 172, 172, 201, 201, 41, 41] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 655 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113219 none O=C(CN1C(=O)CNC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 6, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 158, 201, 201, 201, 201, 201, 201, 33, 33, 33, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 33, 158, 158, 201, 201, 201, 47, 33, 33, 33, 33, 7, 4, 4, 2, 2, 33, 33] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 659 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113219 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113219/1 /scratch/stefan/7770410/working/building/REAL300020113219 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/36 `/scratch/stefan/7770410/working/3D/36' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1C(=O)CNC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113219.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113219 none O=C(CN1C(=O)CNC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 6, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 28, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 8, 8, 8, 21, 33, 33, 33, 33, 33, 8, 8, 1, 28, 28, 41, 41, 41, 6, 1, 1, 1, 1, 8, 21, 21, 33, 33, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 43, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 251 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113219 none O=C(CN1C(=O)CNC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 6, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 90, 127, 127, 127, 127, 127, 127, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 90, 90, 127, 127, 127, 18, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [37, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 402 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113219 none O=C(CN1C(=O)CNC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 6, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 41, 41, 41, 127, 127, 127, 171, 201, 201, 201, 201, 201, 127, 127, 41, 2, 2, 1, 1, 1, 19, 41, 41, 41, 41, 127, 171, 171, 201, 201, 41, 41] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 661 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113219 none O=C(CN1C(=O)CNC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 6, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 158, 201, 201, 201, 201, 201, 201, 33, 33, 33, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 33, 158, 158, 201, 201, 201, 47, 33, 33, 33, 33, 7, 4, 4, 2, 2, 33, 33] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 656 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113219 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113219 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113219/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113219/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113219 Building REAL300020113220 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113220' /scratch/stefan/7770410/working/building/REAL300020113220 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113220 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113220/0 /scratch/stefan/7770410/working/building/REAL300020113220 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/37 `/scratch/stefan/7770410/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC(=O)N(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1=O) `REAL300020113220.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113220 none CN1CC(=O)N(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 41, 30, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 35, 35, 35, 35, 8, 8, 1, 41, 41, 41, 41, 41, 41, 41, 30, 30, 6, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 265 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113220 none CN1CC(=O)N(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 131, 131, 131, 100, 23, 23, 23, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 131, 131, 131, 131, 131, 131, 131, 100, 100, 23, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 423 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113220 none CN1CC(=O)N(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 20, 20, 20, 41, 41, 41, 131, 131, 131, 174, 201, 201, 201, 201, 201, 131, 131, 41, 1, 1, 2, 2, 2, 1, 1, 3, 3, 19, 41, 41, 41, 41, 131, 174, 174, 201, 201, 41, 41] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 26, 27, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 650 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113220 none CN1CC(=O)N(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 166, 57, 57, 57, 35, 35, 35, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 35, 201, 201, 201, 201, 201, 201, 201, 166, 166, 57, 35, 35, 35, 35, 7, 4, 4, 2, 2, 35, 35] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 654 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113220 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113220/1 /scratch/stefan/7770410/working/building/REAL300020113220 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 38) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/38 `/scratch/stefan/7770410/working/3D/38' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC(=O)N(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1=O) `REAL300020113220.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113220/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113220 none CN1CC(=O)N(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 40, 40, 29, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 35, 35, 35, 35, 8, 8, 1, 40, 40, 40, 40, 40, 40, 40, 29, 29, 6, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 262 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113220 none CN1CC(=O)N(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 131, 131, 131, 99, 22, 22, 22, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 131, 131, 131, 131, 131, 131, 131, 99, 99, 22, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 423 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113220 none CN1CC(=O)N(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 20, 20, 20, 40, 40, 40, 131, 131, 131, 174, 201, 201, 201, 201, 201, 131, 131, 40, 1, 1, 2, 2, 2, 1, 1, 3, 3, 19, 40, 40, 40, 40, 131, 174, 174, 201, 201, 40, 40] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 26, 27, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 649 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113220 none CN1CC(=O)N(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 165, 56, 56, 56, 35, 35, 35, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 35, 201, 201, 201, 201, 201, 201, 201, 165, 165, 56, 35, 35, 35, 35, 7, 4, 4, 2, 2, 35, 35] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 654 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113220 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113220 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113220/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113220/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113220 Building REAL300020113221 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113221' /scratch/stefan/7770410/working/building/REAL300020113221 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113221 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113221/0 /scratch/stefan/7770410/working/building/REAL300020113221 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/39 `/scratch/stefan/7770410/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CC=CC=C2N1) `REAL300020113221.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113221 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CC=CC=C2N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 6, 9, 10, 10, 10, 10, 1, 1, 5, 13, 36, 36, 36, 36, 36, 36, 36, 36, 13, 5, 5, 5, 5, 1, 6, 6, 9, 9, 5, 5, 36, 36, 36, 36, 36, 36] 58 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 108 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113221 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CC=CC=C2N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 53, 53, 53, 22, 22, 22, 6, 4, 1, 1, 1, 1, 1, 1, 22, 22, 53, 96, 132, 132, 132, 132, 132, 132, 132, 132, 96, 53, 53, 53, 53, 22, 6, 6, 4, 4, 53, 53, 132, 132, 132, 132, 132, 132] 132 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 330 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113221 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CC=CC=C2N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 18, 26, 27, 27, 27, 27, 5, 5, 1, 5, 20, 20, 20, 20, 20, 20, 20, 20, 5, 1, 1, 1, 1, 5, 18, 18, 26, 26, 1, 1, 20, 20, 20, 20, 20, 20] 58 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113221 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CC=CC=C2N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 20, 20, 20, 36, 36, 36, 52, 58, 58, 58, 58, 58, 36, 36, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 20, 20, 20, 20, 36, 52, 52, 58, 58, 20, 20, 1, 1, 1, 1, 1, 1] 58 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 194 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113221 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113221/1 /scratch/stefan/7770410/working/building/REAL300020113221 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 40) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/40 `/scratch/stefan/7770410/working/3D/40' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CC=CC=C2N1) `REAL300020113221.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113221/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113221 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CC=CC=C2N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 6, 9, 10, 10, 10, 10, 1, 1, 5, 13, 36, 36, 36, 36, 36, 36, 36, 36, 13, 5, 5, 5, 5, 1, 6, 6, 9, 9, 5, 5, 36, 36, 36, 36, 36, 36] 58 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 108 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113221 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CC=CC=C2N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 54, 54, 54, 22, 22, 22, 6, 4, 1, 1, 1, 1, 1, 1, 22, 22, 54, 96, 132, 132, 132, 132, 132, 132, 132, 132, 96, 54, 54, 54, 54, 22, 6, 6, 4, 4, 54, 54, 132, 132, 132, 132, 132, 132] 132 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 332 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113221 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CC=CC=C2N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 18, 26, 27, 27, 27, 27, 5, 5, 1, 5, 20, 20, 20, 20, 20, 20, 20, 20, 5, 1, 1, 1, 1, 5, 18, 18, 26, 26, 1, 1, 20, 20, 20, 20, 20, 20] 58 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113221 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CC=CC=C2N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 20, 20, 20, 36, 36, 36, 52, 58, 58, 58, 58, 58, 36, 36, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 20, 20, 20, 20, 36, 52, 52, 58, 58, 20, 20, 1, 1, 1, 1, 1, 1] 58 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 194 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113221 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113221 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113221/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113221/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113221 Building REAL300020113222 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113222' /scratch/stefan/7770410/working/building/REAL300020113222 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113222 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113222/0 /scratch/stefan/7770410/working/building/REAL300020113222 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/41 `/scratch/stefan/7770410/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)SC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020113222.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113222 none CC1=C(C)SC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 50, 68, 87, 87, 87, 87, 12, 12, 1, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 12, 50, 50, 68, 68, 1, 1, 19] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 332 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113222 none CC1=C(C)SC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 88, 88, 47, 47, 47, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 12, 88, 88, 88, 88, 88, 88, 88, 47, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 88] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 227 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113222 none CC1=C(C)SC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 88, 88, 88, 153, 201, 201, 201, 201, 201, 88, 88, 19, 1, 2, 2, 2, 2, 2, 2, 6, 19, 19, 19, 19, 88, 153, 153, 201, 201, 19, 19, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 44, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 760 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113222 none CC1=C(C)SC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 160, 160, 160, 87, 87, 87, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 87, 201, 201, 201, 201, 201, 201, 201, 160, 87, 87, 87, 87, 17, 6, 6, 4, 4, 87, 87, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 526 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113222 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113222/1 /scratch/stefan/7770410/working/building/REAL300020113222 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 42) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/42 `/scratch/stefan/7770410/working/3D/42' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)SC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020113222.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113222/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113222 none CC1=C(C)SC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 50, 68, 87, 87, 87, 87, 12, 12, 1, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 12, 50, 50, 68, 68, 1, 1, 19] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 332 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113222 none CC1=C(C)SC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 88, 88, 47, 47, 47, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 12, 88, 88, 88, 88, 88, 88, 88, 47, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 88] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 227 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113222 none CC1=C(C)SC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 88, 88, 88, 153, 201, 201, 201, 201, 201, 88, 88, 19, 1, 2, 2, 2, 2, 2, 2, 6, 19, 19, 19, 19, 88, 153, 153, 201, 201, 19, 19, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 44, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 760 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113222 none CC1=C(C)SC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 160, 160, 160, 87, 87, 87, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 87, 201, 201, 201, 201, 201, 201, 201, 160, 87, 87, 87, 87, 17, 6, 6, 4, 4, 87, 87, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 526 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113222 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113222 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113222/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113222/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113222 Building REAL300020113223 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113223' /scratch/stefan/7770410/working/building/REAL300020113223 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113223 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113223/0 /scratch/stefan/7770410/working/building/REAL300020113223 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/43 `/scratch/stefan/7770410/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1CCCCCC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113223.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113223 none O=C(CN1CCCCCC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 28, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 9, 9, 9, 36, 51, 56, 56, 56, 56, 9, 9, 1, 28, 28, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 9, 36, 36, 51, 51, 1, 1] 201 rigid atoms, others: [43, 41, 42, 11, 12, 13, 14, 15, 50, 51, 27, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 310 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113223 none O=C(CN1CCCCCC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 107, 107, 107, 107, 107, 107, 107, 107, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 12, 12, 12, 12, 1, 1, 9, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 32, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9] 201 rigid atoms, others: [45, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 417 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113223 none O=C(CN1CCCCCC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 29, 29, 29, 107, 107, 107, 171, 201, 201, 201, 201, 201, 107, 107, 29, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 29, 29, 29, 29, 107, 171, 171, 201, 201, 29, 29] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 34, 35, 36, 38, 37, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 708 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113223 none O=C(CN1CCCCCC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 201, 201, 201, 201, 201, 201, 201, 201, 56, 56, 56, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 56, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 114, 56, 56, 56, 56, 13, 6, 6, 4, 4, 56, 56] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 738 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113223 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113223/1 /scratch/stefan/7770410/working/building/REAL300020113223 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 44) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/44 `/scratch/stefan/7770410/working/3D/44' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1CCCCCC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113223.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113223/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113223 none O=C(CN1CCCCCC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 28, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 9, 9, 9, 36, 51, 57, 57, 57, 57, 9, 9, 1, 28, 28, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 9, 36, 36, 51, 51, 1, 1] 201 rigid atoms, others: [43, 41, 42, 11, 12, 13, 14, 15, 50, 51, 27, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 312 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113223 none O=C(CN1CCCCCC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 107, 107, 107, 107, 107, 107, 107, 107, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 12, 12, 12, 12, 1, 1, 9, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 32, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9] 201 rigid atoms, others: [45, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 417 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113223 none O=C(CN1CCCCCC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 29, 29, 29, 107, 107, 107, 171, 201, 201, 201, 201, 201, 107, 107, 29, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 29, 29, 29, 29, 107, 171, 171, 201, 201, 29, 29] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 34, 35, 36, 38, 37, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 705 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113223 none O=C(CN1CCCCCC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 116, 201, 201, 201, 201, 201, 201, 201, 201, 57, 57, 57, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 57, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 116, 57, 57, 57, 57, 12, 6, 6, 4, 4, 57, 57] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 734 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113223 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113223 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113223/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113223/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113223 Building REAL300020113224 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113224' /scratch/stefan/7770410/working/building/REAL300020113224 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113224 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113224/0 /scratch/stefan/7770410/working/building/REAL300020113224 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/45 `/scratch/stefan/7770410/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C)SC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020113224.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113224 none CCC1=C(C)SC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 5, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 16, 16, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 42, 59, 70, 70, 70, 70, 11, 11, 1, 16, 26, 26, 26, 26, 26, 16, 16, 16, 6, 1, 1, 1, 1, 11, 42, 42, 59, 59, 1, 1, 16] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47]) total number of confs: 345 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113224 none CCC1=C(C)SC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 5, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 64, 64, 64, 64, 64, 42, 42, 42, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 1, 1, 11, 64, 100, 100, 100, 100, 100, 64, 64, 64, 42, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 64] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 405 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113224 none CCC1=C(C)SC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 5, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 16, 16, 16, 64, 64, 64, 125, 156, 163, 163, 163, 163, 64, 64, 16, 1, 3, 3, 3, 3, 3, 1, 1, 1, 4, 16, 16, 16, 16, 64, 125, 125, 156, 156, 16, 16, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 47, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 592 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113224 none CCC1=C(C)SC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 5, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 163, 163, 163, 163, 163, 154, 154, 154, 70, 70, 70, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 70, 163, 201, 201, 201, 201, 201, 163, 163, 163, 154, 70, 70, 70, 70, 13, 6, 6, 4, 4, 70, 70, 163] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 673 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113224 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113224/1 /scratch/stefan/7770410/working/building/REAL300020113224 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 46) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/46 `/scratch/stefan/7770410/working/3D/46' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C)SC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020113224.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113224/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113224 none CCC1=C(C)SC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 5, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 16, 16, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 42, 59, 70, 70, 70, 70, 11, 11, 1, 16, 26, 26, 26, 26, 26, 16, 16, 16, 6, 1, 1, 1, 1, 11, 42, 42, 59, 59, 1, 1, 16] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47]) total number of confs: 345 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113224 none CCC1=C(C)SC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 5, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 64, 64, 64, 64, 64, 42, 42, 42, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 1, 1, 11, 64, 100, 100, 100, 100, 100, 64, 64, 64, 42, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 64] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 405 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113224 none CCC1=C(C)SC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 5, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 16, 16, 16, 64, 64, 64, 125, 156, 163, 163, 163, 163, 64, 64, 16, 1, 3, 3, 3, 3, 3, 1, 1, 1, 4, 16, 16, 16, 16, 64, 125, 125, 156, 156, 16, 16, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 47, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 592 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113224 none CCC1=C(C)SC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 5, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 163, 163, 163, 163, 163, 154, 154, 154, 70, 70, 70, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 70, 163, 201, 201, 201, 201, 201, 163, 163, 163, 154, 70, 70, 70, 70, 13, 6, 6, 4, 4, 70, 70, 163] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 673 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113224 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113224 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113224/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113224/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113224 Building REAL300020113225 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113225' /scratch/stefan/7770410/working/building/REAL300020113225 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113225 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113225/0 /scratch/stefan/7770410/working/building/REAL300020113225 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/47 `/scratch/stefan/7770410/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C)=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1) `REAL300020113225.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113225 none CC1=NC(C)=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 29, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 22, 30, 35, 35, 35, 35, 6, 6, 1, 29, 29, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 6, 22, 22, 30, 30, 1, 1] 110 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 165 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113225 none CC1=NC(C)=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 55, 55, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 8, 11, 13, 13, 13, 13, 1, 1, 6, 55, 55, 55, 55, 55, 55, 55, 19, 6, 6, 6, 6, 1, 8, 8, 11, 11, 6, 6] 110 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 142 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113225 none CC1=NC(C)=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 29, 29, 29, 55, 55, 55, 97, 110, 110, 110, 110, 110, 55, 55, 29, 1, 2, 2, 2, 2, 2, 2, 9, 29, 29, 29, 29, 55, 97, 97, 110, 110, 29, 29] 110 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 413 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113225 none CC1=NC(C)=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 110, 110, 59, 59, 59, 36, 36, 36, 15, 15, 15, 8, 4, 1, 1, 1, 1, 1, 1, 15, 15, 36, 110, 110, 110, 110, 110, 110, 110, 59, 36, 36, 36, 36, 15, 8, 8, 4, 4, 36, 36] 110 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 259 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113225 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113225/1 /scratch/stefan/7770410/working/building/REAL300020113225 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 48) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/48 `/scratch/stefan/7770410/working/3D/48' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C)=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1) `REAL300020113225.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113225/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113225 none CC1=NC(C)=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 29, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 21, 29, 34, 34, 34, 34, 6, 6, 1, 29, 29, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 6, 21, 21, 29, 29, 1, 1] 109 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 162 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113225 none CC1=NC(C)=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 55, 55, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 6, 55, 55, 55, 55, 55, 55, 55, 19, 6, 6, 6, 6, 1, 8, 8, 10, 10, 6, 6] 109 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 136 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113225 none CC1=NC(C)=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 29, 29, 29, 55, 55, 55, 96, 109, 109, 109, 109, 109, 55, 55, 29, 1, 2, 2, 2, 2, 2, 2, 9, 29, 29, 29, 29, 55, 96, 96, 109, 109, 29, 29] 109 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 410 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113225 none CC1=NC(C)=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 109, 109, 109, 58, 58, 58, 35, 35, 35, 14, 14, 14, 8, 4, 1, 1, 1, 1, 1, 1, 14, 14, 35, 109, 109, 109, 109, 109, 109, 109, 58, 35, 35, 35, 35, 14, 8, 8, 4, 4, 35, 35] 109 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 257 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113225 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113225 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113225/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113225/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113225 Building REAL300020113226 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113226' /scratch/stefan/7770410/working/building/REAL300020113226 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113226 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113226/0 /scratch/stefan/7770410/working/building/REAL300020113226 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/49 `/scratch/stefan/7770410/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1NC(=O)NC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113226.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113226 none O=C(CCC1NC(=O)NC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 11, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 25, 23, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 8, 8, 8, 26, 39, 41, 41, 41, 41, 8, 8, 1, 25, 25, 33, 33, 45, 45, 45, 6, 1, 1, 1, 1, 8, 26, 26, 39, 39, 1, 1] 201 rigid atoms, others: [45, 36, 37, 38, 39, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 371 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113226 none O=C(CCC1NC(=O)NC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 11, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 101, 84, 133, 133, 133, 133, 133, 133, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 101, 101, 120, 120, 133, 133, 133, 26, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [40, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 685 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113226 none O=C(CCC1NC(=O)NC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 11, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 45, 45, 45, 133, 133, 133, 178, 201, 201, 201, 201, 201, 133, 133, 45, 9, 9, 5, 5, 1, 1, 1, 24, 45, 45, 45, 45, 133, 178, 178, 201, 201, 45, 45] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 650 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113226 none O=C(CCC1NC(=O)NC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 11, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 192, 153, 201, 201, 201, 201, 201, 201, 42, 42, 42, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 42, 192, 192, 201, 201, 201, 201, 201, 76, 42, 42, 42, 42, 9, 5, 5, 3, 3, 42, 42] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 983 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113226 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113226/1 /scratch/stefan/7770410/working/building/REAL300020113226 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 50) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/50 `/scratch/stefan/7770410/working/3D/50' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1NC(=O)NC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113226.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113226 none O=C(CCC1NC(=O)NC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 11, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 25, 23, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 8, 8, 8, 26, 39, 40, 40, 40, 40, 8, 8, 1, 25, 25, 33, 33, 45, 45, 45, 6, 1, 1, 1, 1, 8, 26, 26, 39, 39, 1, 1] 201 rigid atoms, others: [45, 36, 37, 38, 39, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 369 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113226 none O=C(CCC1NC(=O)NC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 11, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 102, 84, 134, 134, 134, 134, 134, 134, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 102, 102, 121, 121, 134, 134, 134, 26, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [40, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 693 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113226 none O=C(CCC1NC(=O)NC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 11, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 45, 45, 45, 134, 134, 134, 178, 201, 201, 201, 201, 201, 134, 134, 45, 9, 9, 5, 5, 1, 1, 1, 24, 45, 45, 45, 45, 134, 178, 178, 201, 201, 45, 45] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 645 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113226 none O=C(CCC1NC(=O)NC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 11, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 191, 152, 201, 201, 201, 201, 201, 201, 42, 42, 42, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 42, 191, 191, 201, 201, 201, 201, 201, 76, 42, 42, 42, 42, 9, 5, 5, 3, 3, 42, 42] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 989 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113226 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113226 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113226/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113226/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113226 Building REAL300020113227 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113227' /scratch/stefan/7770410/working/building/REAL300020113227 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113227 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113227/0 /scratch/stefan/7770410/working/building/REAL300020113227 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/51 `/scratch/stefan/7770410/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)NCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113227.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113227 none NC(=O)NCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 117, 117, 117, 75, 17, 17, 17, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 117, 117, 117, 117, 117, 75, 75, 17, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 530 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113227 none NC(=O)NCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 163, 50, 50, 50, 32, 32, 32, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 32, 201, 201, 201, 201, 201, 163, 163, 50, 32, 32, 32, 32, 7, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 843 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113227 none NC(=O)NCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 35, 22, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 21, 33, 33, 33, 33, 33, 8, 8, 1, 36, 36, 36, 35, 35, 22, 22, 5, 1, 1, 1, 1, 8, 21, 21, 33, 33, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 284 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113227 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113227/1 /scratch/stefan/7770410/working/building/REAL300020113227 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 52) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/52 `/scratch/stefan/7770410/working/3D/52' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)NCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113227.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113227/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113227 none NC(=O)NCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 118, 75, 17, 17, 17, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 118, 118, 118, 118, 118, 75, 75, 17, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 536 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113227 none NC(=O)NCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 164, 50, 50, 50, 32, 32, 32, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 32, 201, 201, 201, 201, 201, 164, 164, 50, 32, 32, 32, 32, 7, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 843 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113227 none NC(=O)NCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 35, 22, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 21, 33, 33, 33, 33, 33, 8, 8, 1, 37, 37, 37, 35, 35, 22, 22, 5, 1, 1, 1, 1, 8, 21, 21, 33, 33, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 288 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113227 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113227 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113227/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113227/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113227 Building REAL300020113228 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113228' /scratch/stefan/7770410/working/building/REAL300020113228 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113228 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113228/0 /scratch/stefan/7770410/working/building/REAL300020113228 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/53 `/scratch/stefan/7770410/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1) `REAL300020113228.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113228 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 37, 85, 37, 37, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 85, 114, 114, 94, 114, 114, 85, 85, 85, 85, 85, 85, 37, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 114, 114, 94, 114, 114] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 480 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113228 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 113, 201, 113, 113, 49, 49, 49, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 49, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 113, 49, 49, 49, 49, 10, 5, 5, 3, 3, 49, 49, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 781 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113228 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 6, 21, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 46, 50, 50, 50, 50, 11, 11, 1, 21, 31, 31, 26, 31, 31, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 11, 31, 31, 46, 46, 1, 1, 31, 31, 24, 31, 31] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 44, 45, 21, 38, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113228 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 9, 9, 9, 31, 31, 31, 114, 114, 114, 176, 201, 201, 201, 201, 201, 114, 114, 31, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 9, 31, 31, 31, 31, 114, 176, 176, 201, 201, 31, 31, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 46, 47, 48, 49, 50, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 682 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113228 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113228/1 /scratch/stefan/7770410/working/building/REAL300020113228 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 54) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/54 `/scratch/stefan/7770410/working/3D/54' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1) `REAL300020113228.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113228/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113228 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 37, 84, 37, 37, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 84, 113, 113, 93, 113, 113, 84, 84, 84, 84, 84, 84, 37, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 113, 113, 93, 113, 113] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 474 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113228 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 114, 201, 114, 114, 50, 50, 50, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 50, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 114, 50, 50, 50, 50, 10, 6, 6, 4, 4, 50, 50, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 782 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113228 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 6, 21, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 46, 50, 50, 50, 50, 11, 11, 1, 21, 31, 31, 26, 31, 31, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 11, 31, 31, 46, 46, 1, 1, 31, 31, 24, 31, 31] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 44, 45, 21, 38, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113228 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 9, 9, 9, 31, 31, 31, 113, 113, 113, 176, 201, 201, 201, 201, 201, 113, 113, 31, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 9, 31, 31, 31, 31, 113, 176, 176, 201, 201, 31, 31, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 46, 47, 48, 49, 50, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 686 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113228 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113228 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113228/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113228/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113228 Building REAL300020113229 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113229' /scratch/stefan/7770410/working/building/REAL300020113229 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113229 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113229/0 /scratch/stefan/7770410/working/building/REAL300020113229 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/55 `/scratch/stefan/7770410/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=NC=CN=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113229.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113229 none NC(=O)C1=NC=CN=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 25, 29, 25, 25, 25, 25, 25, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 35, 52, 62, 62, 62, 62, 11, 11, 1, 29, 29, 25, 25, 6, 1, 1, 1, 1, 11, 35, 35, 52, 52, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 42, 11, 12, 13, 14, 15, 43, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 285 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113229 none NC(=O)C1=NC=CN=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 98, 108, 98, 98, 98, 98, 98, 39, 39, 39, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 108, 108, 98, 98, 39, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11] 201 rigid atoms, others: [37, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 260 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113229 none NC(=O)C1=NC=CN=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 25, 25, 25, 98, 98, 98, 162, 195, 195, 195, 195, 195, 98, 98, 25, 4, 4, 1, 1, 8, 25, 25, 25, 25, 98, 162, 162, 195, 195, 25, 25] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 693 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113229 none NC(=O)C1=NC=CN=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 195, 201, 195, 195, 195, 195, 195, 117, 117, 117, 63, 63, 63, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 63, 201, 201, 195, 195, 117, 63, 63, 63, 63, 12, 6, 6, 4, 4, 63, 63] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 478 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113229 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113229/1 /scratch/stefan/7770410/working/building/REAL300020113229 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 56) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/56 `/scratch/stefan/7770410/working/3D/56' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=NC=CN=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113229.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113229/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113229 none NC(=O)C1=NC=CN=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 25, 29, 25, 25, 25, 25, 25, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 35, 52, 62, 62, 62, 62, 11, 11, 1, 29, 29, 25, 25, 6, 1, 1, 1, 1, 11, 35, 35, 52, 52, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 42, 11, 12, 13, 14, 15, 43, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 285 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113229 none NC(=O)C1=NC=CN=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 98, 107, 98, 98, 98, 98, 98, 39, 39, 39, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 107, 107, 98, 98, 39, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11] 201 rigid atoms, others: [37, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 256 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113229 none NC(=O)C1=NC=CN=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 25, 25, 25, 98, 98, 98, 163, 195, 195, 195, 195, 195, 98, 98, 25, 4, 4, 1, 1, 8, 25, 25, 25, 25, 98, 163, 163, 195, 195, 25, 25] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 696 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113229 none NC(=O)C1=NC=CN=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 195, 201, 195, 195, 195, 195, 195, 117, 117, 117, 63, 63, 63, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 63, 201, 201, 195, 195, 117, 63, 63, 63, 63, 12, 6, 6, 4, 4, 63, 63] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 478 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113229 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113229 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113229/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113229/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113229 Building REAL300020113230 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113230' /scratch/stefan/7770410/working/building/REAL300020113230 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113230 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113230/0 /scratch/stefan/7770410/working/building/REAL300020113230 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/57 `/scratch/stefan/7770410/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1C(=O)CCC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113230.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113230 none O=C(CN1C(=O)CCC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 8, 8, 8, 25, 38, 39, 39, 39, 39, 8, 8, 1, 29, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 8, 25, 25, 38, 38, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 44, 10, 11, 12, 13, 14, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 251 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113230 none O=C(CN1C(=O)CCC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 114, 114, 114, 114, 114, 114, 114, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 114, 114, 114, 114, 114, 114, 21, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [38, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 407 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113230 none O=C(CN1C(=O)CCC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 3, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 35, 35, 35, 121, 121, 121, 169, 201, 201, 201, 201, 201, 121, 121, 35, 3, 3, 1, 1, 1, 1, 16, 35, 35, 35, 35, 121, 169, 169, 201, 201, 35, 35] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 672 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113230 none O=C(CN1C(=O)CCC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 201, 201, 201, 201, 201, 201, 201, 37, 37, 37, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 37, 201, 201, 201, 201, 201, 201, 60, 37, 37, 37, 37, 8, 4, 4, 2, 2, 37, 37] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 713 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113230 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113230/1 /scratch/stefan/7770410/working/building/REAL300020113230 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 58) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/58 `/scratch/stefan/7770410/working/3D/58' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1C(=O)CCC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113230.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113230 none O=C(CN1C(=O)CCC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 8, 8, 8, 24, 37, 38, 38, 38, 38, 8, 8, 1, 29, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 8, 24, 24, 37, 37, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 44, 10, 11, 12, 13, 14, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 248 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113230 none O=C(CN1C(=O)CCC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 112, 112, 112, 112, 112, 112, 112, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 8, 8, 8, 8, 1, 1, 8, 112, 112, 112, 112, 112, 112, 21, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [38, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 398 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113230 none O=C(CN1C(=O)CCC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 3, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 34, 34, 34, 119, 119, 119, 170, 201, 201, 201, 201, 201, 119, 119, 34, 3, 3, 1, 1, 1, 1, 16, 34, 34, 34, 34, 119, 170, 170, 201, 201, 34, 34] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 678 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113230 none O=C(CN1C(=O)CCC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 201, 201, 201, 201, 201, 201, 201, 40, 40, 40, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 40, 201, 201, 201, 201, 201, 201, 64, 40, 40, 40, 40, 9, 5, 5, 3, 3, 40, 40] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 718 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113230 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113230 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113230/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113230/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113230 Building REAL300020113231 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113231' /scratch/stefan/7770410/working/building/REAL300020113231 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113231 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113231/0 /scratch/stefan/7770410/working/building/REAL300020113231 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/59 `/scratch/stefan/7770410/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)N1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1) `REAL300020113231.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113231 none NC(=O)N1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 17, 38, 17, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 35, 35, 35, 35, 8, 8, 1, 17, 17, 38, 38, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1, 17, 17, 17, 17] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50]) total number of confs: 255 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113231 none NC(=O)N1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 74, 118, 74, 74, 74, 22, 22, 22, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 74, 74, 118, 118, 74, 74, 74, 74, 74, 22, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8, 74, 74, 74, 74] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 372 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113231 none NC(=O)N1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 6, 6, 7, 17, 17, 17, 74, 74, 74, 116, 152, 152, 152, 152, 152, 74, 74, 17, 1, 1, 5, 5, 1, 1, 1, 1, 1, 7, 17, 17, 17, 17, 74, 116, 116, 152, 152, 17, 17, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 33, 7, 47, 48, 49, 50, 26, 27, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 557 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113231 none NC(=O)N1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 155, 201, 155, 155, 155, 67, 67, 67, 35, 35, 35, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 35, 155, 155, 201, 201, 155, 155, 155, 155, 155, 67, 35, 35, 35, 35, 7, 4, 4, 2, 2, 35, 35, 155, 155, 155, 155] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 626 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113231 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113231/1 /scratch/stefan/7770410/working/building/REAL300020113231 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 60) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/60 `/scratch/stefan/7770410/working/3D/60' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)N1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1) `REAL300020113231.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113231 none NC(=O)N1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 17, 38, 17, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 35, 35, 35, 35, 8, 8, 1, 17, 17, 38, 38, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1, 17, 17, 17, 17] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50]) total number of confs: 255 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113231 none NC(=O)N1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 74, 118, 74, 74, 74, 23, 23, 23, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 74, 74, 118, 118, 74, 74, 74, 74, 74, 23, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8, 74, 74, 74, 74] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 372 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113231 none NC(=O)N1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 6, 6, 7, 17, 17, 17, 74, 74, 74, 116, 152, 152, 152, 152, 152, 74, 74, 17, 1, 1, 5, 5, 1, 1, 1, 1, 1, 7, 17, 17, 17, 17, 74, 116, 116, 152, 152, 17, 17, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 33, 7, 47, 48, 49, 50, 26, 27, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 557 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113231 none NC(=O)N1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 156, 201, 156, 156, 156, 68, 68, 68, 35, 35, 35, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 35, 156, 156, 201, 201, 156, 156, 156, 156, 156, 68, 35, 35, 35, 35, 7, 4, 4, 2, 2, 35, 35, 156, 156, 156, 156] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 624 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113231 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113231 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113231/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113231/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113231 Building REAL300020113232 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113232' /scratch/stefan/7770410/working/building/REAL300020113232 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113232 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113232/0 /scratch/stefan/7770410/working/building/REAL300020113232 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/61 `/scratch/stefan/7770410/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1) `REAL300020113232.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113232 none CC(=O)N1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 16, 31, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 24, 37, 37, 37, 37, 37, 8, 8, 1, 16, 16, 31, 31, 31, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 8, 24, 24, 37, 37, 1, 1, 16, 16, 16, 16] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 248 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113232 none CC(=O)N1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 62, 104, 62, 62, 62, 23, 23, 23, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 62, 62, 104, 104, 104, 62, 62, 62, 62, 62, 23, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 62, 62, 62, 62] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 363 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113232 none CC(=O)N1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 62, 62, 62, 102, 133, 133, 133, 133, 133, 62, 62, 16, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 7, 16, 16, 16, 16, 62, 102, 102, 133, 133, 16, 16, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 33, 7, 48, 49, 50, 35, 26, 27, 51, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 516 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113232 none CC(=O)N1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 134, 201, 134, 134, 134, 69, 69, 69, 37, 37, 37, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 37, 134, 134, 201, 201, 201, 134, 134, 134, 134, 134, 69, 37, 37, 37, 37, 8, 4, 4, 2, 2, 37, 37, 134, 134, 134, 134] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 663 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113232 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113232/1 /scratch/stefan/7770410/working/building/REAL300020113232 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 62) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/62 `/scratch/stefan/7770410/working/3D/62' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1) `REAL300020113232.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113232 none CC(=O)N1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 16, 31, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 24, 37, 37, 37, 37, 37, 8, 8, 1, 16, 16, 31, 31, 31, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 8, 24, 24, 37, 37, 1, 1, 16, 16, 16, 16] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 248 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113232 none CC(=O)N1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 62, 104, 62, 62, 62, 23, 23, 23, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 62, 62, 104, 104, 104, 62, 62, 62, 62, 62, 23, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 62, 62, 62, 62] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 363 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113232 none CC(=O)N1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 62, 62, 62, 102, 133, 133, 133, 133, 133, 62, 62, 16, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 7, 16, 16, 16, 16, 62, 102, 102, 133, 133, 16, 16, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 33, 7, 48, 49, 50, 35, 26, 27, 51, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 516 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113232 none CC(=O)N1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 134, 201, 134, 134, 134, 69, 69, 69, 37, 37, 37, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 37, 134, 134, 201, 201, 201, 134, 134, 134, 134, 134, 69, 37, 37, 37, 37, 8, 4, 4, 2, 2, 37, 37, 134, 134, 134, 134] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 659 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113232 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113232 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113232/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113232/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113232 Building REAL300020113233 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113233' /scratch/stefan/7770410/working/building/REAL300020113233 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113233 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113233/0 /scratch/stefan/7770410/working/building/REAL300020113233 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/63 `/scratch/stefan/7770410/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC2=NC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CN21) `REAL300020113233.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113233 none CC1=CC=CC2=NC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 71, 92, 115, 115, 115, 115, 13, 13, 1, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 71, 71, 92, 92, 1, 1, 16] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47]) total number of confs: 423 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113233 none CC1=CC=CC2=NC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 87, 87, 87, 87, 53, 53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 20, 20, 20, 20, 1, 1, 13, 87, 87, 87, 87, 87, 87, 87, 87, 53, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 87] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 257 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113233 none CC1=CC=CC2=NC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 87, 87, 87, 167, 201, 201, 201, 201, 201, 87, 87, 16, 1, 1, 2, 2, 2, 1, 1, 1, 6, 16, 16, 16, 16, 87, 167, 167, 201, 201, 16, 16, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 7, 34, 47, 27, 28, 5] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 699 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113233 none CC1=CC=CC2=NC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 197, 197, 197, 117, 117, 117, 24, 24, 24, 6, 4, 1, 1, 1, 1, 1, 1, 24, 24, 117, 201, 201, 201, 201, 201, 201, 201, 201, 197, 117, 117, 117, 117, 24, 6, 6, 4, 4, 117, 117, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 532 number of broken/clashed sets: 2 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113233 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113233/1 /scratch/stefan/7770410/working/building/REAL300020113233 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 64) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/64 `/scratch/stefan/7770410/working/3D/64' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC2=NC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CN21) `REAL300020113233.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113233 none CC1=CC=CC2=NC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 71, 93, 117, 117, 117, 117, 13, 13, 1, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 71, 71, 93, 93, 1, 1, 16] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47]) total number of confs: 431 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113233 none CC1=CC=CC2=NC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 87, 87, 87, 87, 54, 54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 20, 20, 20, 20, 1, 1, 13, 87, 87, 87, 87, 87, 87, 87, 87, 54, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 87] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 257 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113233 none CC1=CC=CC2=NC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 87, 87, 87, 166, 201, 201, 201, 201, 201, 87, 87, 16, 1, 1, 2, 2, 2, 1, 1, 1, 6, 16, 16, 16, 16, 87, 166, 166, 201, 201, 16, 16, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 7, 34, 47, 27, 28, 5] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 703 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113233 none CC1=CC=CC2=NC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 198, 198, 198, 118, 118, 118, 24, 24, 24, 6, 4, 1, 1, 1, 1, 1, 1, 24, 24, 118, 201, 201, 201, 201, 201, 201, 201, 201, 198, 118, 118, 118, 118, 24, 6, 6, 4, 4, 118, 118, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 532 number of broken/clashed sets: 2 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113233 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113233 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113233/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113233/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113233 Building REAL300020113234 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113234' /scratch/stefan/7770410/working/building/REAL300020113234 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113234 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113234/0 /scratch/stefan/7770410/working/building/REAL300020113234 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/65 `/scratch/stefan/7770410/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113234.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113234 none CC1=CC=CC=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 28, 28, 19, 4, 4, 4, 1, 1, 1, 1, 1, 7, 7, 7, 21, 33, 33, 33, 33, 33, 7, 7, 1, 28, 28, 28, 28, 28, 28, 28, 19, 19, 4, 1, 1, 1, 1, 7, 21, 21, 33, 33, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 217 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113234 none CC1=CC=CC=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 108, 108, 108, 74, 14, 14, 14, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 108, 108, 108, 108, 108, 108, 108, 74, 74, 14, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 352 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113234 none CC1=CC=CC=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 28, 28, 28, 108, 108, 108, 162, 201, 201, 201, 201, 201, 108, 108, 28, 2, 2, 2, 1, 1, 1, 1, 5, 5, 16, 28, 28, 28, 28, 108, 162, 162, 201, 201, 28, 28] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 33, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 716 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113234 none CC1=CC=CC=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 141, 45, 45, 45, 33, 33, 33, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 33, 201, 201, 201, 201, 201, 201, 201, 141, 141, 45, 33, 33, 33, 33, 7, 4, 4, 2, 2, 33, 33] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 652 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113234 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113234/1 /scratch/stefan/7770410/working/building/REAL300020113234 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 66) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/66 `/scratch/stefan/7770410/working/3D/66' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113234.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113234 none CC1=CC=CC=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 28, 28, 19, 4, 4, 4, 1, 1, 1, 1, 1, 7, 7, 7, 21, 33, 33, 33, 33, 33, 7, 7, 1, 28, 28, 28, 28, 28, 28, 28, 19, 19, 4, 1, 1, 1, 1, 7, 21, 21, 33, 33, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 217 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113234 none CC1=CC=CC=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 109, 109, 109, 109, 75, 14, 14, 14, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 109, 109, 109, 109, 109, 109, 109, 75, 75, 14, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 355 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113234 none CC1=CC=CC=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 28, 28, 28, 109, 109, 109, 163, 201, 201, 201, 201, 201, 109, 109, 28, 2, 2, 2, 1, 1, 1, 1, 5, 5, 16, 28, 28, 28, 28, 109, 163, 163, 201, 201, 28, 28] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 33, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 712 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113234 none CC1=CC=CC=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 141, 45, 45, 45, 33, 33, 33, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 33, 201, 201, 201, 201, 201, 201, 201, 141, 141, 45, 33, 33, 33, 33, 7, 4, 4, 2, 2, 33, 33] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 649 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113234 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113234 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113234/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113234/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113234 Building REAL300020113235 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113235' /scratch/stefan/7770410/working/building/REAL300020113235 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113235 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113235/0 /scratch/stefan/7770410/working/building/REAL300020113235 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/67 `/scratch/stefan/7770410/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)NC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020113235.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113235 none NC(=O)NC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 27, 38, 9, 9, 9, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 7, 7, 7, 21, 33, 33, 33, 33, 33, 7, 7, 1, 9, 38, 38, 27, 9, 9, 9, 3, 1, 1, 1, 1, 7, 21, 21, 33, 33, 1, 1, 9] 201 rigid atoms, others: [45, 36, 37, 38, 39, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47]) total number of confs: 250 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113235 none NC(=O)NC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 77, 109, 33, 33, 33, 33, 33, 13, 13, 13, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 33, 109, 109, 77, 33, 33, 33, 13, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7, 33] 201 rigid atoms, others: [40, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 369 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113235 none NC(=O)NC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 9, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 33, 33, 33, 68, 96, 96, 96, 96, 96, 33, 33, 9, 1, 9, 9, 5, 1, 1, 1, 5, 9, 9, 9, 9, 33, 68, 68, 96, 96, 9, 9, 1] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 47, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 433 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113235 none NC(=O)NC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 161, 201, 96, 96, 96, 96, 96, 43, 43, 43, 33, 33, 33, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 33, 96, 201, 201, 161, 96, 96, 96, 43, 33, 33, 33, 33, 8, 4, 4, 2, 2, 33, 33, 96] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 595 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113235 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113235/1 /scratch/stefan/7770410/working/building/REAL300020113235 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 68) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/68 `/scratch/stefan/7770410/working/3D/68' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)NC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020113235.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113235 none NC(=O)NC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 26, 37, 9, 9, 9, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 7, 7, 7, 21, 33, 33, 33, 33, 33, 7, 7, 1, 9, 37, 37, 26, 9, 9, 9, 3, 1, 1, 1, 1, 7, 21, 21, 33, 33, 1, 1, 9] 201 rigid atoms, others: [45, 36, 37, 38, 39, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47]) total number of confs: 248 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113235 none NC(=O)NC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 76, 109, 33, 33, 33, 33, 33, 13, 13, 13, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 33, 109, 109, 76, 33, 33, 33, 13, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7, 33] 201 rigid atoms, others: [40, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 371 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113235 none NC(=O)NC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 9, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 33, 33, 33, 68, 96, 96, 96, 96, 96, 33, 33, 9, 1, 9, 9, 5, 1, 1, 1, 5, 9, 9, 9, 9, 33, 68, 68, 96, 96, 9, 9, 1] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 47, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 433 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113235 none NC(=O)NC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 160, 201, 96, 96, 96, 96, 96, 43, 43, 43, 33, 33, 33, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 33, 96, 201, 201, 160, 96, 96, 96, 43, 33, 33, 33, 33, 8, 4, 4, 2, 2, 33, 33, 96] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 595 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113235 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113235 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113235/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113235/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113235 Building REAL300020113236 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113236' /scratch/stefan/7770410/working/building/REAL300020113236 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113236 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113236/0 /scratch/stefan/7770410/working/building/REAL300020113236 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/69 `/scratch/stefan/7770410/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(OC)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020113236.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113236 none COC1=CC=C(OC)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 34, 34, 34, 34, 34, 34, 44, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 33, 41, 50, 50, 50, 50, 7, 7, 1, 34, 45, 45, 45, 34, 34, 44, 44, 44, 6, 1, 1, 1, 1, 7, 33, 33, 41, 41, 1, 1, 34] 201 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49]) total number of confs: 257 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113236 none COC1=CC=C(OC)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 71, 71, 71, 71, 71, 71, 87, 28, 28, 28, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 7, 71, 99, 99, 99, 71, 71, 87, 87, 87, 28, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7, 71] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 262 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113236 none COC1=CC=C(OC)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 3, 1, 1, 12, 12, 12, 34, 34, 34, 71, 71, 71, 147, 167, 185, 185, 185, 185, 71, 71, 34, 1, 3, 3, 3, 1, 1, 4, 4, 4, 12, 34, 34, 34, 34, 71, 147, 147, 167, 167, 34, 34, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 8, 9, 49, 28] set([0, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 633 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113236 none COC1=CC=C(OC)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 189, 189, 189, 189, 189, 189, 201, 127, 127, 127, 64, 64, 64, 24, 24, 24, 7, 4, 1, 1, 1, 1, 1, 1, 24, 24, 64, 189, 201, 201, 201, 189, 189, 201, 201, 201, 127, 64, 64, 64, 64, 24, 7, 7, 4, 4, 64, 64, 189] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 510 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113236 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113236/1 /scratch/stefan/7770410/working/building/REAL300020113236 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 70) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/70 `/scratch/stefan/7770410/working/3D/70' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(OC)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020113236.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113236/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113236 none COC1=CC=C(OC)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 34, 34, 34, 34, 34, 34, 44, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 34, 42, 51, 51, 51, 51, 7, 7, 1, 34, 45, 45, 45, 34, 34, 44, 44, 44, 6, 1, 1, 1, 1, 7, 34, 34, 42, 42, 1, 1, 34] 201 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49]) total number of confs: 260 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113236 none COC1=CC=C(OC)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 73, 73, 73, 73, 73, 73, 89, 28, 28, 28, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 7, 73, 101, 101, 101, 73, 73, 89, 89, 89, 28, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7, 73] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 264 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113236 none COC1=CC=C(OC)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 3, 1, 1, 12, 12, 12, 34, 34, 34, 73, 73, 73, 149, 169, 186, 186, 186, 186, 73, 73, 34, 1, 3, 3, 3, 1, 1, 4, 4, 4, 12, 34, 34, 34, 34, 73, 149, 149, 169, 169, 34, 34, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 8, 9, 49, 28] set([0, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 633 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113236 none COC1=CC=C(OC)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 189, 189, 189, 189, 189, 189, 201, 127, 127, 127, 64, 64, 64, 24, 24, 24, 7, 4, 1, 1, 1, 1, 1, 1, 24, 24, 64, 189, 201, 201, 201, 189, 189, 201, 201, 201, 127, 64, 64, 64, 64, 24, 7, 7, 4, 4, 64, 64, 189] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 510 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113236 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113236 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113236/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113236/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113236 Building REAL300020113237 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113237' /scratch/stefan/7770410/working/building/REAL300020113237 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113237 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113237/0 /scratch/stefan/7770410/working/building/REAL300020113237 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/71 `/scratch/stefan/7770410/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CC=CS1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113237.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113237 none O=C(CCC1=CC=CS1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 32, 41, 62, 62, 62, 62, 1, 1, 1, 1, 1, 9, 9, 9, 17, 25, 25, 25, 25, 25, 9, 9, 1, 32, 32, 41, 41, 62, 62, 62, 6, 1, 1, 1, 1, 9, 17, 17, 25, 25, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 301 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113237 none O=C(CCC1=CC=CS1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 91, 108, 132, 132, 132, 132, 9, 9, 9, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 9, 91, 91, 108, 108, 132, 132, 132, 28, 9, 9, 9, 9, 1, 5, 5, 7, 7, 9, 9] 201 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 500 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113237 none O=C(CCC1=CC=CS1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 5, 3, 1, 1, 1, 1, 1, 1, 23, 23, 62, 62, 62, 132, 132, 132, 174, 201, 201, 201, 201, 201, 132, 132, 62, 5, 5, 3, 3, 1, 1, 1, 23, 62, 62, 62, 62, 132, 174, 174, 201, 201, 62, 62] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 681 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113237 none O=C(CCC1=CC=CS1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 161, 177, 201, 201, 201, 200, 25, 25, 25, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 25, 161, 161, 177, 177, 201, 201, 201, 71, 25, 25, 25, 25, 7, 4, 4, 2, 2, 25, 25] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 750 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113237 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113237/1 /scratch/stefan/7770410/working/building/REAL300020113237 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 72) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/72 `/scratch/stefan/7770410/working/3D/72' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CC=CS1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113237.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113237/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113237 none O=C(CCC1=CC=CS1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 33, 42, 63, 63, 63, 63, 1, 1, 1, 1, 1, 9, 9, 9, 17, 25, 25, 25, 25, 25, 9, 9, 1, 33, 33, 42, 42, 63, 63, 63, 6, 1, 1, 1, 1, 9, 17, 17, 25, 25, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 304 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113237 none O=C(CCC1=CC=CS1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 93, 110, 134, 134, 134, 134, 9, 9, 9, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 9, 93, 93, 110, 110, 134, 134, 134, 29, 9, 9, 9, 9, 1, 5, 5, 7, 7, 9, 9] 201 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 508 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113237 none O=C(CCC1=CC=CS1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 5, 3, 1, 1, 1, 1, 1, 1, 23, 23, 63, 63, 63, 134, 134, 134, 175, 201, 201, 201, 201, 201, 134, 134, 63, 5, 5, 3, 3, 1, 1, 1, 23, 63, 63, 63, 63, 134, 175, 175, 201, 201, 63, 63] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 678 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113237 none O=C(CCC1=CC=CS1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 160, 176, 201, 201, 201, 200, 25, 25, 25, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 25, 160, 160, 176, 176, 201, 201, 201, 72, 25, 25, 25, 25, 7, 4, 4, 2, 2, 25, 25] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 748 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113237 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113237 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113237/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113237/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113237 Building REAL300020113238 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113238' /scratch/stefan/7770410/working/building/REAL300020113238 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113238 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113238/0 /scratch/stefan/7770410/working/building/REAL300020113238 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/73 `/scratch/stefan/7770410/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1) `REAL300020113238.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113238 none CC(C)CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 5, 5, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 30, 44, 45, 45, 45, 45, 11, 11, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 11, 30, 30, 44, 44, 1, 1, 14, 14] 201 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 44, 50, 51, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 255 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113238 none CC(C)CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 23, 24, 74, 74, 23, 23, 23, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 74, 74, 74, 74, 74, 74, 74, 74, 74, 74, 74, 74, 74, 23, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 74, 74] 201 rigid atoms, others: [45, 14, 13, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 468 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113238 none CC(C)CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 74, 74, 74, 148, 201, 201, 201, 201, 201, 74, 74, 14, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 5, 14, 14, 14, 14, 74, 148, 148, 201, 201, 14, 14, 1, 1] 201 rigid atoms, others: [3, 4, 5, 38, 7, 8, 39, 52, 53, 6, 27, 28] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 802 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113238 none CC(C)CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 71, 74, 201, 201, 71, 71, 71, 46, 46, 46, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 46, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 71, 46, 46, 46, 46, 9, 5, 5, 3, 3, 46, 46, 201, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 1200 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113238 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113238/1 /scratch/stefan/7770410/working/building/REAL300020113238 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 74) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/74 `/scratch/stefan/7770410/working/3D/74' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1) `REAL300020113238.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113238 none CC(C)CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 5, 5, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 30, 44, 45, 45, 45, 45, 11, 11, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 11, 30, 30, 44, 44, 1, 1, 14, 14] 201 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 44, 50, 51, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 255 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113238 none CC(C)CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 24, 25, 75, 75, 24, 24, 24, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 75, 75, 75, 75, 75, 75, 75, 75, 75, 75, 75, 75, 75, 24, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 75, 75] 201 rigid atoms, others: [45, 14, 13, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 470 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113238 none CC(C)CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 75, 75, 75, 148, 201, 201, 201, 201, 201, 75, 75, 14, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 5, 14, 14, 14, 14, 75, 148, 148, 201, 201, 14, 14, 1, 1] 201 rigid atoms, others: [3, 4, 5, 38, 7, 8, 39, 52, 53, 6, 27, 28] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 801 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113238 none CC(C)CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 71, 75, 201, 201, 71, 71, 71, 45, 45, 45, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 45, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 71, 45, 45, 45, 45, 9, 5, 5, 3, 3, 45, 45, 201, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 1200 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113238 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113238 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113238/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113238/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113238 Building REAL300020113239 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113239' /scratch/stefan/7770410/working/building/REAL300020113239 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113239 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113239/0 /scratch/stefan/7770410/working/building/REAL300020113239 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/75 `/scratch/stefan/7770410/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1C=CC=CC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113239.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113239 none O=C(CN1C=CC=CC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 26, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 9, 9, 9, 33, 46, 49, 49, 49, 49, 9, 9, 1, 26, 26, 28, 28, 28, 28, 6, 1, 1, 1, 1, 9, 33, 33, 46, 46, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 44, 10, 11, 12, 13, 14, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 281 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113239 none O=C(CN1C=CC=CC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 91, 102, 102, 102, 102, 102, 102, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 91, 91, 102, 102, 102, 102, 27, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [38, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 374 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113239 none O=C(CN1C=CC=CC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 3, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 28, 28, 28, 102, 102, 102, 169, 201, 201, 201, 201, 201, 102, 102, 28, 3, 3, 1, 1, 1, 1, 11, 28, 28, 28, 28, 102, 169, 169, 201, 201, 28, 28] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 720 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113239 none O=C(CN1C=CC=CC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 189, 201, 201, 201, 201, 201, 201, 49, 49, 49, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 49, 189, 189, 201, 201, 201, 201, 92, 49, 49, 49, 49, 10, 6, 6, 4, 4, 49, 49] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 722 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113239 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113239/1 /scratch/stefan/7770410/working/building/REAL300020113239 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 76) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/76 `/scratch/stefan/7770410/working/3D/76' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1C=CC=CC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113239.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113239 none O=C(CN1C=CC=CC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 26, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 9, 9, 9, 33, 46, 49, 49, 49, 49, 9, 9, 1, 26, 26, 28, 28, 28, 28, 6, 1, 1, 1, 1, 9, 33, 33, 46, 46, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 44, 10, 11, 12, 13, 14, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 281 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113239 none O=C(CN1C=CC=CC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 91, 102, 102, 102, 102, 102, 102, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 91, 91, 102, 102, 102, 102, 27, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [38, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 374 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113239 none O=C(CN1C=CC=CC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 3, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 28, 28, 28, 102, 102, 102, 169, 201, 201, 201, 201, 201, 102, 102, 28, 3, 3, 1, 1, 1, 1, 11, 28, 28, 28, 28, 102, 169, 169, 201, 201, 28, 28] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 720 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113239 none O=C(CN1C=CC=CC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 189, 201, 201, 201, 201, 201, 201, 49, 49, 49, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 49, 189, 189, 201, 201, 201, 201, 92, 49, 49, 49, 49, 10, 6, 6, 4, 4, 49, 49] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 722 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113239 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113239 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113239/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113239/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113239 Building REAL300020113240 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113240' /scratch/stefan/7770410/working/building/REAL300020113240 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113240 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113240/0 /scratch/stefan/7770410/working/building/REAL300020113240 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/77 `/scratch/stefan/7770410/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2CCCC2=C1) `REAL300020113240.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113240 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2CCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 27, 75, 75, 75, 75, 75, 75, 75, 75, 27, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 75, 75, 75, 75, 75, 75, 75, 75, 75] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 169 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113240 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2CCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 46, 46, 46, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 46, 78, 201, 201, 201, 201, 201, 201, 201, 201, 78, 46, 46, 46, 46, 12, 6, 6, 4, 4, 46, 46, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 393 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113240 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2CCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 29, 42, 45, 45, 45, 45, 9, 9, 1, 6, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 9, 29, 29, 42, 42, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113240 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2CCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 17, 17, 17, 75, 75, 75, 148, 201, 201, 201, 201, 201, 75, 75, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 17, 17, 17, 17, 75, 148, 148, 201, 201, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 802 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113240 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113240/1 /scratch/stefan/7770410/working/building/REAL300020113240 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 78) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/78 `/scratch/stefan/7770410/working/3D/78' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2CCCC2=C1) `REAL300020113240.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113240 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2CCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 27, 75, 75, 75, 75, 75, 75, 75, 75, 27, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 75, 75, 75, 75, 75, 75, 75, 75, 75] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 169 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113240 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2CCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 46, 46, 46, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 46, 78, 201, 201, 201, 201, 201, 201, 201, 201, 78, 46, 46, 46, 46, 12, 6, 6, 4, 4, 46, 46, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 393 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113240 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2CCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 29, 42, 45, 45, 45, 45, 9, 9, 1, 6, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 9, 29, 29, 42, 42, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113240 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2CCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 17, 17, 17, 75, 75, 75, 148, 201, 201, 201, 201, 201, 75, 75, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 17, 17, 17, 17, 75, 148, 148, 201, 201, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 802 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113240 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113240 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113240/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113240/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113240 Building REAL300020113241 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113241' /scratch/stefan/7770410/working/building/REAL300020113241 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113241 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113241/0 /scratch/stefan/7770410/working/building/REAL300020113241 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/79 `/scratch/stefan/7770410/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C)=C1CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113241.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113241 none CC1=NOC(C)=C1CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 53, 31, 31, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 10, 14, 14, 14, 14, 14, 6, 6, 1, 53, 53, 53, 53, 53, 53, 31, 31, 31, 31, 6, 1, 1, 1, 1, 6, 10, 10, 14, 14, 1, 1] 72 rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 14, 15, 48, 49, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 198 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113241 none CC1=NOC(C)=C1CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 69, 69, 69, 41, 41, 17, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 4, 6, 6, 6, 6, 6, 1, 1, 6, 69, 69, 69, 69, 69, 69, 41, 41, 41, 41, 17, 6, 6, 6, 6, 1, 4, 4, 6, 6, 6, 6] 72 rigid atoms, others: [43, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 228 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113241 none CC1=NOC(C)=C1CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 19, 19, 19, 53, 53, 53, 69, 69, 69, 71, 72, 72, 72, 72, 72, 69, 69, 53, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 19, 53, 53, 53, 53, 69, 71, 71, 72, 72, 53, 53] 72 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 208 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113241 none CC1=NOC(C)=C1CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 72, 72, 72, 45, 45, 27, 27, 27, 16, 16, 16, 10, 10, 10, 6, 2, 1, 1, 1, 1, 1, 1, 10, 10, 16, 72, 72, 72, 72, 72, 72, 45, 45, 45, 45, 27, 16, 16, 16, 16, 10, 6, 6, 2, 2, 16, 16] 72 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 220 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113241 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113241/1 /scratch/stefan/7770410/working/building/REAL300020113241 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 80) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/80 `/scratch/stefan/7770410/working/3D/80' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C)=C1CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113241.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113241/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113241 none CC1=NOC(C)=C1CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 53, 31, 31, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 10, 13, 13, 13, 13, 13, 6, 6, 1, 53, 53, 53, 53, 53, 53, 31, 31, 31, 31, 6, 1, 1, 1, 1, 6, 10, 10, 13, 13, 1, 1] 71 rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 14, 15, 48, 49, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 192 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113241 none CC1=NOC(C)=C1CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 69, 69, 69, 41, 41, 17, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 4, 6, 6, 6, 6, 6, 1, 1, 6, 69, 69, 69, 69, 69, 69, 41, 41, 41, 41, 17, 6, 6, 6, 6, 1, 4, 4, 6, 6, 6, 6] 71 rigid atoms, others: [43, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 228 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113241 none CC1=NOC(C)=C1CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 19, 19, 19, 53, 53, 53, 69, 69, 69, 71, 71, 71, 71, 71, 71, 69, 69, 53, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 19, 53, 53, 53, 53, 69, 71, 71, 71, 71, 53, 53] 71 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 202 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113241 none CC1=NOC(C)=C1CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 72, 72, 72, 45, 45, 27, 27, 27, 16, 16, 16, 10, 10, 10, 6, 2, 1, 1, 1, 1, 1, 1, 10, 10, 16, 72, 72, 72, 72, 72, 72, 45, 45, 45, 45, 27, 16, 16, 16, 16, 10, 6, 6, 2, 2, 16, 16] 72 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 220 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113241 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113241 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113241/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113241/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113241 Building REAL300020113242 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113242' /scratch/stefan/7770410/working/building/REAL300020113242 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113242 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113242/0 /scratch/stefan/7770410/working/building/REAL300020113242 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/81 `/scratch/stefan/7770410/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1) `REAL300020113242.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113242 none COCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 28, 12, 5, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 24, 36, 36, 36, 36, 36, 8, 8, 1, 12, 12, 38, 38, 38, 28, 28, 12, 12, 5, 1, 1, 1, 1, 8, 24, 24, 36, 36, 1, 1, 12, 12] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 282 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113242 none COCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 77, 42, 19, 42, 42, 19, 19, 19, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 42, 42, 97, 97, 97, 77, 77, 42, 42, 19, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 42, 42] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 425 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113242 none COCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 42, 42, 42, 97, 134, 134, 134, 134, 134, 42, 42, 12, 1, 1, 8, 8, 8, 4, 4, 1, 1, 5, 12, 12, 12, 12, 42, 97, 97, 134, 134, 12, 12, 1, 1] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 47, 48, 26, 27] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 579 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113242 none COCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 153, 70, 153, 153, 70, 70, 70, 40, 40, 40, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 40, 153, 153, 201, 201, 201, 201, 201, 153, 153, 70, 40, 40, 40, 40, 10, 6, 6, 4, 4, 40, 40, 153, 153] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 930 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113242 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113242/1 /scratch/stefan/7770410/working/building/REAL300020113242 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 82) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/82 `/scratch/stefan/7770410/working/3D/82' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1) `REAL300020113242.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113242 none COCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 28, 12, 5, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 23, 35, 35, 35, 35, 35, 7, 7, 1, 12, 12, 38, 38, 38, 28, 28, 12, 12, 5, 1, 1, 1, 1, 7, 23, 23, 35, 35, 1, 1, 12, 12] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 281 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113242 none COCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 76, 41, 18, 41, 41, 18, 18, 18, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 41, 41, 96, 96, 96, 76, 76, 41, 41, 18, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7, 41, 41] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 423 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113242 none COCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 41, 41, 41, 96, 134, 134, 134, 134, 134, 41, 41, 12, 1, 1, 8, 8, 8, 4, 4, 1, 1, 5, 12, 12, 12, 12, 41, 96, 96, 134, 134, 12, 12, 1, 1] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 47, 48, 26, 27] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 584 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113242 none COCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 152, 69, 152, 152, 69, 69, 69, 38, 38, 38, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 38, 152, 152, 201, 201, 201, 201, 201, 152, 152, 69, 38, 38, 38, 38, 10, 6, 6, 4, 4, 38, 38, 152, 152] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 931 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113242 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113242 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113242/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113242/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113242 Building REAL300020113243 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113243' /scratch/stefan/7770410/working/building/REAL300020113243 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113243 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113243/0 /scratch/stefan/7770410/working/building/REAL300020113243 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/83 `/scratch/stefan/7770410/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=NO1) `REAL300020113243.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113243 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 24, 36, 36, 36, 36, 36, 9, 9, 1, 22, 22, 22, 22, 32, 32, 32, 32, 32, 6, 1, 1, 1, 1, 9, 24, 24, 36, 36, 1, 1, 22, 22, 22] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 229 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113243 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 92, 92, 26, 26, 26, 9, 9, 9, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 9, 92, 92, 92, 92, 125, 125, 125, 125, 125, 26, 9, 9, 9, 9, 1, 5, 5, 7, 7, 9, 9, 92, 92, 92] 201 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 349 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113243 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 10, 10, 10, 22, 22, 22, 92, 92, 92, 141, 181, 181, 181, 181, 181, 92, 92, 22, 1, 1, 1, 1, 5, 5, 5, 5, 5, 10, 22, 22, 22, 22, 92, 141, 141, 181, 181, 22, 22, 2, 2, 2] 201 rigid atoms, others: [1, 2, 3, 4, 23, 24, 25, 26] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 652 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113243 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 181, 181, 65, 65, 65, 36, 36, 36, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 36, 181, 181, 181, 181, 201, 201, 201, 201, 201, 65, 36, 36, 36, 36, 7, 4, 4, 2, 2, 36, 36, 181, 181, 181] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 467 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113243 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113243/1 /scratch/stefan/7770410/working/building/REAL300020113243 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 84) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/84 `/scratch/stefan/7770410/working/3D/84' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=NO1) `REAL300020113243.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113243 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 24, 36, 36, 36, 36, 36, 9, 9, 1, 22, 22, 22, 22, 32, 32, 32, 32, 32, 6, 1, 1, 1, 1, 9, 24, 24, 36, 36, 1, 1, 22, 22, 22] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 229 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113243 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 92, 92, 26, 26, 26, 9, 9, 9, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 9, 92, 92, 92, 92, 125, 125, 125, 125, 125, 26, 9, 9, 9, 9, 1, 5, 5, 7, 7, 9, 9, 92, 92, 92] 201 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 349 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113243 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 10, 10, 10, 22, 22, 22, 92, 92, 92, 141, 181, 181, 181, 181, 181, 92, 92, 22, 1, 1, 1, 1, 5, 5, 5, 5, 5, 10, 22, 22, 22, 22, 92, 141, 141, 181, 181, 22, 22, 2, 2, 2] 201 rigid atoms, others: [1, 2, 3, 4, 23, 24, 25, 26] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 652 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113243 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 181, 181, 65, 65, 65, 36, 36, 36, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 36, 181, 181, 181, 181, 201, 201, 201, 201, 201, 65, 36, 36, 36, 36, 7, 4, 4, 2, 2, 36, 36, 181, 181, 181] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 467 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113243 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113243 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113243/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113243/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113243 Building REAL300020113244 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113244' /scratch/stefan/7770410/working/building/REAL300020113244 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113244 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113244/0 /scratch/stefan/7770410/working/building/REAL300020113244 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/85 `/scratch/stefan/7770410/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1N=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CC1=O) `REAL300020113244.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113244 none CCCN1N=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 27, 14, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 29, 42, 45, 45, 45, 45, 9, 9, 1, 14, 14, 14, 14, 34, 34, 34, 34, 34, 27, 27, 6, 1, 1, 1, 1, 9, 29, 29, 42, 42, 1, 1, 14, 14] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 46, 47, 40, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49]) total number of confs: 322 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113244 none CCCN1N=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 104, 57, 57, 57, 29, 29, 29, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 11, 11, 11, 11, 1, 1, 9, 57, 57, 57, 57, 112, 112, 112, 112, 112, 104, 104, 29, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 57, 57] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 486 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113244 none CCCN1N=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 57, 57, 57, 95, 118, 118, 118, 118, 118, 57, 57, 14, 1, 1, 1, 1, 5, 5, 5, 5, 5, 3, 3, 5, 14, 14, 14, 14, 57, 95, 95, 118, 118, 14, 14, 1, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 48, 49, 25, 26, 27, 28] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 440 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113244 none CCCN1N=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 118, 118, 118, 101, 101, 101, 45, 45, 45, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 45, 118, 118, 118, 118, 201, 201, 201, 201, 201, 201, 201, 101, 45, 45, 45, 45, 11, 6, 6, 4, 4, 45, 45, 118, 118] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 817 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113244 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113244/1 /scratch/stefan/7770410/working/building/REAL300020113244 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 86) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/86 `/scratch/stefan/7770410/working/3D/86' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1N=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CC1=O) `REAL300020113244.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113244 none CCCN1N=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 27, 14, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 29, 42, 45, 45, 45, 45, 9, 9, 1, 14, 14, 14, 14, 34, 34, 34, 34, 34, 27, 27, 6, 1, 1, 1, 1, 9, 29, 29, 42, 42, 1, 1, 14, 14] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 46, 47, 40, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49]) total number of confs: 322 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113244 none CCCN1N=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 105, 56, 56, 56, 29, 29, 29, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 11, 11, 11, 11, 1, 1, 9, 56, 56, 56, 56, 113, 113, 113, 113, 113, 105, 105, 29, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 56, 56] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 497 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113244 none CCCN1N=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 56, 56, 56, 93, 116, 116, 116, 116, 116, 56, 56, 14, 1, 1, 1, 1, 5, 5, 5, 5, 5, 3, 3, 5, 14, 14, 14, 14, 56, 93, 93, 116, 116, 14, 14, 1, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 48, 49, 25, 26, 27, 28] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 433 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113244 none CCCN1N=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 117, 117, 117, 100, 100, 100, 47, 47, 47, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 47, 117, 117, 117, 117, 201, 201, 201, 201, 201, 201, 201, 100, 47, 47, 47, 47, 12, 6, 6, 4, 4, 47, 47, 117, 117] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 823 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113244 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113244 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113244/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113244/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113244 Building REAL300020113245 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113245' /scratch/stefan/7770410/working/building/REAL300020113245 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113245 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113245/0 /scratch/stefan/7770410/working/building/REAL300020113245 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/87 `/scratch/stefan/7770410/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COC1=CC=C(F)C=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113245.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113245 none O=C(COC1=CC=C(F)C=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 16, 39, 44, 44, 39, 39, 44, 44, 1, 1, 1, 1, 1, 8, 8, 8, 30, 43, 45, 45, 45, 45, 8, 8, 1, 16, 16, 44, 44, 44, 44, 5, 1, 1, 1, 1, 8, 30, 30, 43, 43, 1, 1] 201 rigid atoms, others: [45, 35, 36, 37, 38, 44, 11, 12, 13, 14, 15, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 285 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113245 none O=C(COC1=CC=C(F)C=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 57, 118, 120, 120, 119, 119, 120, 120, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 57, 57, 120, 120, 120, 120, 22, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [39, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 341 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113245 none O=C(COC1=CC=C(F)C=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 44, 44, 44, 120, 120, 120, 171, 201, 201, 201, 201, 201, 120, 120, 44, 8, 8, 1, 1, 1, 1, 21, 44, 44, 44, 44, 120, 171, 171, 201, 201, 44, 44] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 687 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113245 none O=C(COC1=CC=C(F)C=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 147, 201, 201, 201, 201, 201, 201, 201, 46, 46, 46, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 46, 147, 147, 201, 201, 201, 201, 81, 46, 46, 46, 46, 10, 5, 5, 3, 3, 46, 46] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 635 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113245 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113245/1 /scratch/stefan/7770410/working/building/REAL300020113245 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 88) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/88 `/scratch/stefan/7770410/working/3D/88' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COC1=CC=C(F)C=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113245.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113245/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113245 none O=C(COC1=CC=C(F)C=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 17, 40, 46, 46, 40, 40, 46, 46, 1, 1, 1, 1, 1, 8, 8, 8, 30, 43, 45, 45, 45, 45, 8, 8, 1, 17, 17, 46, 46, 46, 46, 6, 1, 1, 1, 1, 8, 30, 30, 43, 43, 1, 1] 201 rigid atoms, others: [45, 35, 36, 37, 38, 44, 11, 12, 13, 14, 15, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 292 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113245 none O=C(COC1=CC=C(F)C=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 58, 119, 122, 122, 120, 120, 122, 122, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 58, 58, 122, 122, 122, 122, 23, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [39, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 348 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113245 none O=C(COC1=CC=C(F)C=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 46, 46, 46, 122, 122, 122, 171, 201, 201, 201, 201, 201, 122, 122, 46, 8, 8, 1, 1, 1, 1, 22, 46, 46, 46, 46, 122, 171, 171, 201, 201, 46, 46] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 682 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113245 none O=C(COC1=CC=C(F)C=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 145, 201, 201, 201, 201, 201, 201, 201, 45, 45, 45, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 45, 145, 145, 201, 201, 201, 201, 80, 45, 45, 45, 45, 9, 5, 5, 3, 3, 45, 45] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 631 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113245 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113245 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113245/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113245/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113245 Building REAL300020113246 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113246' /scratch/stefan/7770410/working/building/REAL300020113246 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113246 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113246/0 /scratch/stefan/7770410/working/building/REAL300020113246 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/89 `/scratch/stefan/7770410/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=NNN=C2C=C1) `REAL300020113246.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113246 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=NNN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 26, 73, 73, 73, 73, 73, 73, 73, 73, 26, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9, 73, 73, 73, 73] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 171 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113246 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=NNN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 55, 55, 55, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 55, 86, 201, 201, 201, 201, 201, 201, 201, 201, 86, 55, 55, 55, 55, 12, 6, 6, 4, 4, 55, 55, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 420 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113246 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=NNN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 32, 46, 53, 53, 53, 53, 9, 9, 1, 5, 15, 15, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 9, 32, 32, 46, 46, 1, 1, 15, 15, 15, 15] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 225 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113246 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=NNN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 15, 15, 15, 73, 73, 73, 149, 201, 201, 201, 201, 201, 73, 73, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 73, 149, 149, 201, 201, 15, 15, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 810 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113246 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113246/1 /scratch/stefan/7770410/working/building/REAL300020113246 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 90) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/90 `/scratch/stefan/7770410/working/3D/90' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=NNN=C2C=C1) `REAL300020113246.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113246 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=NNN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 26, 73, 73, 73, 73, 73, 73, 73, 73, 26, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9, 73, 73, 73, 73] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 171 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113246 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=NNN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 55, 55, 55, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 55, 87, 201, 201, 201, 201, 201, 201, 201, 201, 87, 55, 55, 55, 55, 12, 6, 6, 4, 4, 55, 55, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 422 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113246 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=NNN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 32, 46, 53, 53, 53, 53, 9, 9, 1, 5, 15, 15, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 9, 32, 32, 46, 46, 1, 1, 15, 15, 15, 15] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 225 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113246 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=NNN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 15, 15, 15, 73, 73, 73, 149, 201, 201, 201, 201, 201, 73, 73, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 73, 149, 149, 201, 201, 15, 15, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 810 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113246 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113246 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113246/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113246/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113246 Building REAL300020113247 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113247' /scratch/stefan/7770410/working/building/REAL300020113247 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113247 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113247/0 /scratch/stefan/7770410/working/building/REAL300020113247 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/91 `/scratch/stefan/7770410/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=C1) `REAL300020113247.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113247 none CC1=CC=C(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 29, 39, 39, 25, 9, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 19, 31, 31, 31, 31, 31, 7, 7, 1, 39, 39, 39, 39, 39, 39, 39, 39, 9, 9, 5, 1, 1, 1, 1, 7, 19, 19, 31, 31, 1, 1, 39, 39, 39, 39] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 306 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113247 none CC1=CC=C(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 96, 111, 111, 84, 31, 15, 15, 15, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 111, 111, 111, 111, 111, 111, 111, 111, 31, 31, 15, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 111, 111, 111, 111] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 483 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113247 none CC1=CC=C(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 13, 23, 23, 23, 39, 39, 39, 111, 111, 111, 165, 201, 201, 201, 201, 201, 111, 111, 39, 1, 1, 1, 2, 2, 2, 1, 1, 13, 13, 23, 39, 39, 39, 39, 111, 165, 165, 201, 201, 39, 39, 2, 2, 2, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 51, 26, 27, 28, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 762 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113247 none CC1=CC=C(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [172, 191, 201, 201, 172, 75, 46, 46, 46, 32, 32, 32, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 32, 201, 201, 201, 201, 201, 201, 201, 201, 75, 75, 46, 32, 32, 32, 32, 8, 4, 4, 2, 2, 32, 32, 201, 201, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 716 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113247 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113247/1 /scratch/stefan/7770410/working/building/REAL300020113247 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 92) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/92 `/scratch/stefan/7770410/working/3D/92' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=C1) `REAL300020113247.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113247 none CC1=CC=C(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 29, 39, 39, 25, 9, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 19, 31, 31, 31, 31, 31, 7, 7, 1, 39, 39, 39, 39, 39, 39, 39, 39, 9, 9, 5, 1, 1, 1, 1, 7, 19, 19, 31, 31, 1, 1, 39, 39, 39, 39] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 306 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113247 none CC1=CC=C(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 97, 112, 112, 85, 32, 15, 15, 15, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 112, 112, 112, 112, 112, 112, 112, 112, 32, 32, 15, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 112, 112, 112, 112] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 486 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113247 none CC1=CC=C(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 13, 23, 23, 23, 39, 39, 39, 112, 112, 112, 165, 201, 201, 201, 201, 201, 112, 112, 39, 1, 1, 1, 2, 2, 2, 1, 1, 13, 13, 23, 39, 39, 39, 39, 112, 165, 165, 201, 201, 39, 39, 2, 2, 2, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 51, 26, 27, 28, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 759 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113247 none CC1=CC=C(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [172, 189, 201, 201, 172, 73, 45, 45, 45, 31, 31, 31, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 31, 201, 201, 201, 201, 201, 201, 201, 201, 73, 73, 45, 31, 31, 31, 31, 7, 4, 4, 2, 2, 31, 31, 201, 201, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 712 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113247 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113247 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113247/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113247/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113247 Building REAL300020113248 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113248' /scratch/stefan/7770410/working/building/REAL300020113248 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113248 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113248/0 /scratch/stefan/7770410/working/building/REAL300020113248 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/93 `/scratch/stefan/7770410/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C)=C1CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113248.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113248 none CC1=NNC(C)=C1CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 23, 5, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 26, 40, 44, 44, 44, 44, 10, 10, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 23, 23, 5, 1, 1, 1, 1, 10, 26, 26, 40, 40, 1, 1] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 260 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113248 none CC1=NNC(C)=C1CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 103, 103, 103, 103, 102, 25, 25, 25, 10, 10, 10, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 10, 103, 103, 103, 103, 103, 103, 103, 103, 103, 102, 102, 25, 10, 10, 10, 10, 1, 5, 5, 7, 7, 10, 10] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 384 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113248 none CC1=NNC(C)=C1CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 20, 21, 21, 41, 41, 41, 136, 136, 136, 185, 201, 201, 201, 201, 201, 136, 136, 41, 2, 2, 2, 1, 2, 2, 2, 2, 2, 4, 4, 21, 41, 41, 41, 41, 136, 185, 185, 201, 201, 41, 41] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 631 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113248 none CC1=NNC(C)=C1CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 77, 77, 77, 44, 44, 44, 9, 9, 9, 6, 4, 1, 1, 1, 1, 1, 1, 9, 9, 44, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 77, 44, 44, 44, 44, 9, 6, 6, 4, 4, 44, 44] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 755 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113248 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113248/1 /scratch/stefan/7770410/working/building/REAL300020113248 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 94) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/94 `/scratch/stefan/7770410/working/3D/94' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C)=C1CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113248.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113248 none CC1=NNC(C)=C1CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 23, 5, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 26, 40, 44, 44, 44, 44, 10, 10, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 23, 23, 5, 1, 1, 1, 1, 10, 26, 26, 40, 40, 1, 1] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 260 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113248 none CC1=NNC(C)=C1CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 102, 102, 102, 102, 101, 25, 25, 25, 10, 10, 10, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 10, 102, 102, 102, 102, 102, 102, 102, 102, 102, 101, 101, 25, 10, 10, 10, 10, 1, 5, 5, 7, 7, 10, 10] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 381 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113248 none CC1=NNC(C)=C1CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 20, 21, 21, 41, 41, 41, 135, 135, 135, 185, 201, 201, 201, 201, 201, 135, 135, 41, 2, 2, 2, 1, 2, 2, 2, 2, 2, 4, 4, 21, 41, 41, 41, 41, 135, 185, 185, 201, 201, 41, 41] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 636 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113248 none CC1=NNC(C)=C1CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 77, 77, 77, 44, 44, 44, 9, 9, 9, 6, 4, 1, 1, 1, 1, 1, 1, 9, 9, 44, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 77, 44, 44, 44, 44, 9, 6, 6, 4, 4, 44, 44] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 755 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113248 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113248 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113248/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113248/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113248 Building REAL300020113249 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113249' /scratch/stefan/7770410/working/building/REAL300020113249 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113249 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113249/0 /scratch/stefan/7770410/working/building/REAL300020113249 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/95 `/scratch/stefan/7770410/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113249.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113249 none O=C(COCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 15, 17, 33, 49, 49, 39, 49, 49, 1, 1, 1, 1, 1, 7, 7, 7, 21, 33, 33, 33, 33, 33, 7, 7, 1, 15, 15, 33, 33, 49, 49, 49, 49, 49, 5, 1, 1, 1, 1, 7, 21, 21, 33, 33, 1, 1] 201 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 356 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113249 none O=C(COCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 52, 55, 89, 113, 113, 100, 113, 113, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 52, 52, 89, 89, 113, 113, 113, 113, 113, 21, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 519 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113249 none O=C(COCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 17, 10, 3, 1, 1, 1, 1, 1, 1, 1, 27, 27, 49, 49, 49, 113, 113, 113, 171, 201, 201, 201, 201, 201, 113, 113, 49, 17, 17, 3, 3, 1, 1, 1, 1, 1, 27, 49, 49, 49, 49, 113, 171, 171, 201, 201, 49, 49] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 36] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 744 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113249 none O=C(COCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 130, 133, 201, 201, 201, 201, 201, 201, 35, 35, 35, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 35, 130, 130, 201, 201, 201, 201, 201, 201, 201, 63, 35, 35, 35, 35, 9, 4, 4, 2, 2, 35, 35] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 891 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113249 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113249/1 /scratch/stefan/7770410/working/building/REAL300020113249 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 96) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/96 `/scratch/stefan/7770410/working/3D/96' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113249.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113249 none O=C(COCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 15, 17, 32, 48, 48, 39, 48, 48, 1, 1, 1, 1, 1, 7, 7, 7, 21, 33, 33, 33, 33, 33, 7, 7, 1, 15, 15, 32, 32, 48, 48, 48, 48, 48, 5, 1, 1, 1, 1, 7, 21, 21, 33, 33, 1, 1] 201 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 348 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113249 none O=C(COCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 53, 56, 88, 113, 113, 100, 113, 113, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 53, 53, 88, 88, 113, 113, 113, 113, 113, 21, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 521 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113249 none O=C(COCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 16, 8, 3, 1, 1, 1, 1, 1, 1, 1, 26, 26, 48, 48, 48, 113, 113, 113, 171, 201, 201, 201, 201, 201, 113, 113, 48, 16, 16, 3, 3, 1, 1, 1, 1, 1, 26, 48, 48, 48, 48, 113, 171, 171, 201, 201, 48, 48] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 36] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 750 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113249 none O=C(COCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 130, 133, 201, 201, 201, 201, 201, 201, 34, 34, 34, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 34, 130, 130, 201, 201, 201, 201, 201, 201, 201, 62, 34, 34, 34, 34, 8, 4, 4, 2, 2, 34, 34] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 896 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113249 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113249 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113249/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113249/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113249 Building REAL300020113250 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113250' /scratch/stefan/7770410/working/building/REAL300020113250 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113250 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113250/0 /scratch/stefan/7770410/working/building/REAL300020113250 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/97 `/scratch/stefan/7770410/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1) `REAL300020113250.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113250 none NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 6, 18, 6, 18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 37, 54, 63, 63, 63, 63, 11, 11, 1, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 11, 37, 37, 54, 54, 1, 1, 18, 18] 201 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45]) total number of confs: 322 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113250 none NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 40, 97, 40, 97, 97, 40, 40, 40, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 11, 97, 97, 97, 97, 97, 97, 40, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 97, 97] 201 rigid atoms, others: [37, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 491 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113250 none NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 97, 97, 97, 174, 201, 201, 201, 201, 201, 97, 97, 18, 1, 1, 2, 2, 1, 1, 5, 18, 18, 18, 18, 97, 174, 174, 201, 201, 18, 18, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 26, 27, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 711 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113250 none NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 135, 201, 135, 201, 201, 135, 135, 135, 64, 64, 64, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 64, 201, 201, 201, 201, 201, 201, 135, 64, 64, 64, 64, 12, 6, 6, 4, 4, 64, 64, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 978 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113250 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113250/1 /scratch/stefan/7770410/working/building/REAL300020113250 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 98) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/98 `/scratch/stefan/7770410/working/3D/98' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1) `REAL300020113250.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113250/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113250 none NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 6, 18, 6, 18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 39, 56, 63, 63, 63, 63, 11, 11, 1, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 11, 39, 39, 56, 56, 1, 1, 18, 18] 201 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45]) total number of confs: 324 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113250 none NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 40, 98, 40, 98, 98, 40, 40, 40, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 98, 98, 98, 98, 98, 98, 40, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 98, 98] 201 rigid atoms, others: [37, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 493 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113250 none NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 98, 98, 98, 175, 201, 201, 201, 201, 201, 98, 98, 18, 1, 1, 2, 2, 1, 1, 5, 18, 18, 18, 18, 98, 175, 175, 201, 201, 18, 18, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 26, 27, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 707 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113250 none NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 135, 201, 135, 201, 201, 135, 135, 135, 64, 64, 64, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 64, 201, 201, 201, 201, 201, 201, 135, 64, 64, 64, 64, 12, 6, 6, 4, 4, 64, 64, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 978 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113250 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113250 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113250/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113250/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113250 Building REAL300020113251 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113251' /scratch/stefan/7770410/working/building/REAL300020113251 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113251 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113251/0 /scratch/stefan/7770410/working/building/REAL300020113251 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/99 `/scratch/stefan/7770410/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=C2CCCC2=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113251.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113251 none O=C(CC1=CC=C2CCCC2=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 13, 25, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 7, 7, 7, 19, 31, 31, 31, 31, 31, 7, 7, 1, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 1, 1, 1, 1, 7, 19, 19, 31, 31, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 218 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113251 none O=C(CC1=CC=C2CCCC2=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 55, 99, 119, 119, 119, 119, 119, 119, 119, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 55, 55, 119, 119, 119, 119, 119, 119, 119, 119, 119, 21, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 401 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113251 none O=C(CC1=CC=C2CCCC2=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 29, 29, 29, 119, 119, 119, 163, 201, 201, 201, 201, 201, 119, 119, 29, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 29, 29, 29, 29, 119, 163, 163, 201, 201, 29, 29] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 36, 38, 37, 39, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 663 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113251 none O=C(CC1=CC=C2CCCC2=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 103, 180, 201, 201, 201, 201, 201, 201, 201, 33, 33, 33, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 33, 103, 103, 201, 201, 201, 201, 201, 201, 201, 201, 201, 55, 33, 33, 33, 33, 8, 4, 4, 2, 2, 33, 33] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 630 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113251 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113251/1 /scratch/stefan/7770410/working/building/REAL300020113251 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 100) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/100 `/scratch/stefan/7770410/working/3D/100' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=C2CCCC2=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113251.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113251 none O=C(CC1=CC=C2CCCC2=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 13, 25, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 7, 7, 7, 19, 31, 31, 31, 31, 31, 7, 7, 1, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 1, 1, 1, 1, 7, 19, 19, 31, 31, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 218 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113251 none O=C(CC1=CC=C2CCCC2=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 55, 98, 118, 118, 118, 118, 118, 118, 118, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 55, 55, 118, 118, 118, 118, 118, 118, 118, 118, 118, 21, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 400 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113251 none O=C(CC1=CC=C2CCCC2=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 29, 29, 29, 118, 118, 118, 162, 201, 201, 201, 201, 201, 118, 118, 29, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 29, 29, 29, 29, 118, 162, 162, 201, 201, 29, 29] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 36, 38, 37, 39, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 667 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113251 none O=C(CC1=CC=C2CCCC2=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 103, 181, 201, 201, 201, 201, 201, 201, 201, 32, 32, 32, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 32, 103, 103, 201, 201, 201, 201, 201, 201, 201, 201, 201, 54, 32, 32, 32, 32, 8, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 630 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113251 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113251 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113251/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113251/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113251 Building REAL300020113252 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113252' /scratch/stefan/7770410/working/building/REAL300020113252 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113252 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113252/0 /scratch/stefan/7770410/working/building/REAL300020113252 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/101 `/scratch/stefan/7770410/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(NC(=O)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1) `REAL300020113252.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113252 none CC1=CC=C(NC(=O)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 11, 20, 20, 10, 10, 6, 10, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 56, 74, 89, 89, 89, 89, 11, 11, 1, 20, 20, 20, 20, 20, 20, 20, 10, 6, 1, 1, 1, 1, 11, 56, 56, 74, 74, 1, 1, 20, 20] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 423 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113252 none CC1=CC=C(NC(=O)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 56, 92, 92, 52, 52, 46, 52, 46, 46, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 11, 92, 92, 92, 92, 92, 92, 92, 52, 46, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 92, 92] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 538 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113252 none CC1=CC=C(NC(=O)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 11, 11, 27, 27, 27, 105, 105, 105, 165, 201, 201, 201, 201, 201, 105, 105, 27, 1, 1, 2, 2, 2, 1, 1, 7, 11, 27, 27, 27, 27, 105, 165, 165, 201, 201, 27, 27, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 47, 48, 27, 28, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 700 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113252 none CC1=CC=C(NC(=O)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 185, 185, 178, 185, 178, 178, 88, 88, 88, 16, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 88, 201, 201, 201, 201, 201, 201, 201, 185, 178, 88, 88, 88, 88, 16, 6, 6, 4, 4, 88, 88, 201, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 556 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113252 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113252/1 /scratch/stefan/7770410/working/building/REAL300020113252 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 102) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/102 `/scratch/stefan/7770410/working/3D/102' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(NC(=O)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1) `REAL300020113252.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113252 none CC1=CC=C(NC(=O)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 20, 20, 10, 10, 6, 10, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 56, 74, 89, 89, 89, 89, 11, 11, 1, 20, 20, 20, 20, 20, 20, 20, 10, 6, 1, 1, 1, 1, 11, 56, 56, 74, 74, 1, 1, 20, 20] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 421 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113252 none CC1=CC=C(NC(=O)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 56, 91, 91, 52, 52, 46, 52, 46, 46, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 11, 91, 91, 91, 91, 91, 91, 91, 52, 46, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 91, 91] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 527 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113252 none CC1=CC=C(NC(=O)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 26, 26, 26, 105, 105, 105, 165, 201, 201, 201, 201, 201, 105, 105, 26, 1, 1, 2, 2, 2, 1, 1, 6, 10, 26, 26, 26, 26, 105, 165, 165, 201, 201, 26, 26, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 47, 48, 27, 28, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 699 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113252 none CC1=CC=C(NC(=O)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 185, 185, 178, 185, 178, 178, 88, 88, 88, 16, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 88, 201, 201, 201, 201, 201, 201, 201, 185, 178, 88, 88, 88, 88, 16, 6, 6, 4, 4, 88, 88, 201, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 556 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113252 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113252 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113252/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113252/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113252 Building REAL300020113253 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113253' /scratch/stefan/7770410/working/building/REAL300020113253 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113253 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113253/0 /scratch/stefan/7770410/working/building/REAL300020113253 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/103 `/scratch/stefan/7770410/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CC=CC=C1F)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113253.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113253 none O=C(CCC1=CC=CC=C1F)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 21, 27, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 8, 8, 8, 21, 32, 32, 32, 32, 32, 8, 8, 1, 21, 21, 27, 27, 36, 36, 36, 36, 5, 1, 1, 1, 1, 8, 21, 21, 32, 32, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 256 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113253 none O=C(CCC1=CC=CC=C1F)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 89, 103, 120, 120, 120, 120, 120, 120, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 89, 89, 103, 103, 120, 120, 120, 120, 20, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 450 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113253 none O=C(CCC1=CC=CC=C1F)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 36, 36, 36, 120, 120, 120, 165, 201, 201, 201, 201, 201, 120, 120, 36, 5, 5, 3, 3, 1, 1, 1, 1, 21, 36, 36, 36, 36, 120, 165, 165, 201, 201, 36, 36] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 35] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 696 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113253 none O=C(CCC1=CC=CC=C1F)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 177, 187, 201, 201, 201, 201, 201, 201, 34, 34, 34, 10, 10, 10, 5, 2, 1, 1, 1, 1, 1, 1, 10, 10, 34, 177, 177, 187, 187, 201, 201, 201, 201, 55, 34, 34, 34, 34, 10, 5, 5, 2, 2, 34, 34] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 721 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113253 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113253/1 /scratch/stefan/7770410/working/building/REAL300020113253 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 104) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/104 `/scratch/stefan/7770410/working/3D/104' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CC=CC=C1F)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113253.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113253/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113253 none O=C(CCC1=CC=CC=C1F)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 21, 27, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 8, 8, 8, 21, 32, 32, 32, 32, 32, 8, 8, 1, 21, 21, 27, 27, 36, 36, 36, 36, 5, 1, 1, 1, 1, 8, 21, 21, 32, 32, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 256 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113253 none O=C(CCC1=CC=CC=C1F)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 89, 103, 120, 120, 120, 120, 120, 120, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 89, 89, 103, 103, 120, 120, 120, 120, 20, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 450 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113253 none O=C(CCC1=CC=CC=C1F)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 36, 36, 36, 120, 120, 120, 165, 201, 201, 201, 201, 201, 120, 120, 36, 5, 5, 3, 3, 1, 1, 1, 1, 21, 36, 36, 36, 36, 120, 165, 165, 201, 201, 36, 36] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 35] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 696 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113253 none O=C(CCC1=CC=CC=C1F)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 176, 186, 201, 201, 201, 201, 201, 201, 34, 34, 34, 10, 10, 10, 5, 2, 1, 1, 1, 1, 1, 1, 10, 10, 34, 176, 176, 186, 186, 201, 201, 201, 201, 55, 34, 34, 34, 34, 10, 5, 5, 2, 2, 34, 34] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 720 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113253 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113253 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113253/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113253/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113253 Building REAL300020113254 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113254' /scratch/stefan/7770410/working/building/REAL300020113254 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113254 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113254/0 /scratch/stefan/7770410/working/building/REAL300020113254 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/105 `/scratch/stefan/7770410/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CSC(=O)N1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113254.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113254 none CC1=CSC(=O)N1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 30, 30, 28, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 28, 41, 43, 43, 43, 43, 9, 9, 1, 30, 30, 30, 30, 28, 28, 6, 1, 1, 1, 1, 9, 28, 28, 41, 41, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 44, 10, 11, 12, 13, 14, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 267 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113254 none CC1=CSC(=O)N1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 103, 103, 103, 93, 26, 26, 26, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 9, 103, 103, 103, 103, 93, 93, 26, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [38, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 380 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113254 none CC1=CSC(=O)N1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 30, 30, 30, 103, 103, 103, 170, 201, 201, 201, 201, 201, 103, 103, 30, 1, 1, 1, 1, 2, 2, 13, 30, 30, 30, 30, 103, 170, 170, 201, 201, 30, 30] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 27, 28, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 716 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113254 none CC1=CSC(=O)N1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 191, 88, 88, 88, 43, 43, 43, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 43, 201, 201, 201, 201, 191, 191, 88, 43, 43, 43, 43, 9, 5, 5, 3, 3, 43, 43] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 747 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113254 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113254/1 /scratch/stefan/7770410/working/building/REAL300020113254 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 106) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/106 `/scratch/stefan/7770410/working/3D/106' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CSC(=O)N1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113254.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113254/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113254 none CC1=CSC(=O)N1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 30, 30, 28, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 28, 41, 43, 43, 43, 43, 9, 9, 1, 30, 30, 30, 30, 28, 28, 6, 1, 1, 1, 1, 9, 28, 28, 41, 41, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 44, 10, 11, 12, 13, 14, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 267 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113254 none CC1=CSC(=O)N1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 104, 104, 104, 93, 26, 26, 26, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 9, 104, 104, 104, 104, 93, 93, 26, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [38, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 382 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113254 none CC1=CSC(=O)N1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 30, 30, 30, 104, 104, 104, 170, 201, 201, 201, 201, 201, 104, 104, 30, 1, 1, 1, 1, 2, 2, 13, 30, 30, 30, 30, 104, 170, 170, 201, 201, 30, 30] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 27, 28, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 708 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113254 none CC1=CSC(=O)N1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 190, 89, 89, 89, 44, 44, 44, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 44, 201, 201, 201, 201, 190, 190, 89, 44, 44, 44, 44, 10, 6, 6, 4, 4, 44, 44] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 746 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113254 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113254 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113254/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113254/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113254 Building REAL300020113255 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113255' /scratch/stefan/7770410/working/building/REAL300020113255 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113255 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113255/0 /scratch/stefan/7770410/working/building/REAL300020113255 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/107 `/scratch/stefan/7770410/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C)=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113255.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113255 none CC1=NOC(C)=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 69, 69, 69, 34, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 12, 12, 12, 12, 12, 12, 11, 11, 1, 69, 69, 69, 69, 69, 69, 34, 34, 6, 1, 1, 1, 1, 11, 12, 12, 12, 12, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 193 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113255 none CC1=NOC(C)=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 115, 40, 40, 40, 11, 11, 11, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 11, 201, 201, 201, 201, 201, 201, 115, 115, 40, 11, 11, 11, 11, 1, 3, 3, 3, 3, 11, 11] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 598 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113255 none CC1=NOC(C)=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 27, 27, 27, 69, 69, 69, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 69, 2, 2, 2, 2, 2, 2, 5, 5, 27, 69, 69, 69, 69, 201, 201, 201, 201, 201, 69, 69] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 382 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113255 none CC1=NOC(C)=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 115, 40, 40, 40, 12, 12, 12, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 201, 201, 201, 201, 201, 201, 115, 115, 40, 12, 12, 12, 12, 3, 3, 3, 1, 1, 12, 12] 201 rigid atoms, others: [43, 44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46]) total number of confs: 598 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113255 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113255/1 /scratch/stefan/7770410/working/building/REAL300020113255 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 108) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/108 `/scratch/stefan/7770410/working/3D/108' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C)=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113255.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113255 none CC1=NOC(C)=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 69, 69, 69, 34, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 12, 12, 12, 12, 12, 12, 11, 11, 1, 69, 69, 69, 69, 69, 69, 34, 34, 6, 1, 1, 1, 1, 11, 12, 12, 12, 12, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 193 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113255 none CC1=NOC(C)=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 115, 40, 40, 40, 11, 11, 11, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 11, 201, 201, 201, 201, 201, 201, 115, 115, 40, 11, 11, 11, 11, 1, 3, 3, 3, 3, 11, 11] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 598 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113255 none CC1=NOC(C)=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 27, 27, 27, 69, 69, 69, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 69, 2, 2, 2, 2, 2, 2, 5, 5, 27, 69, 69, 69, 69, 201, 201, 201, 201, 201, 69, 69] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 382 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113255 none CC1=NOC(C)=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 115, 40, 40, 40, 12, 12, 12, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 201, 201, 201, 201, 201, 201, 115, 115, 40, 12, 12, 12, 12, 3, 3, 3, 1, 1, 12, 12] 201 rigid atoms, others: [43, 44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46]) total number of confs: 598 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113255 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113255 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113255/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113255/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113255 Building REAL300020113256 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113256' /scratch/stefan/7770410/working/building/REAL300020113256 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113256 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113256/0 /scratch/stefan/7770410/working/building/REAL300020113256 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/109 `/scratch/stefan/7770410/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C)=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113256.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113256 none CC1=NNC(C)=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 5, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 30, 44, 46, 46, 46, 46, 10, 10, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5, 1, 1, 1, 1, 10, 30, 30, 44, 44, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 271 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113256 none CC1=NNC(C)=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 109, 109, 109, 109, 109, 27, 27, 27, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 10, 109, 109, 109, 109, 109, 109, 109, 109, 109, 27, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 407 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113256 none CC1=NNC(C)=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 20, 20, 20, 42, 42, 42, 134, 134, 134, 185, 201, 201, 201, 201, 201, 134, 134, 42, 2, 2, 2, 1, 2, 2, 2, 2, 2, 20, 42, 42, 42, 42, 134, 185, 185, 201, 201, 42, 42] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 630 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113256 none CC1=NNC(C)=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 85, 85, 85, 47, 47, 47, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 47, 201, 201, 201, 201, 201, 201, 201, 201, 201, 85, 47, 47, 47, 47, 10, 6, 6, 4, 4, 47, 47] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 760 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113256 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113256/1 /scratch/stefan/7770410/working/building/REAL300020113256 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 110) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/110 `/scratch/stefan/7770410/working/3D/110' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C)=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113256.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113256/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113256 none CC1=NNC(C)=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 5, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 31, 45, 47, 47, 47, 47, 10, 10, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5, 1, 1, 1, 1, 10, 31, 31, 45, 45, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 274 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113256 none CC1=NNC(C)=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 108, 108, 108, 108, 27, 27, 27, 10, 10, 10, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 10, 108, 108, 108, 108, 108, 108, 108, 108, 108, 27, 10, 10, 10, 10, 1, 7, 7, 9, 9, 10, 10] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 409 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113256 none CC1=NNC(C)=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 20, 20, 20, 42, 42, 42, 134, 134, 134, 185, 201, 201, 201, 201, 201, 134, 134, 42, 2, 2, 2, 1, 2, 2, 2, 2, 2, 20, 42, 42, 42, 42, 134, 185, 185, 201, 201, 42, 42] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 630 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113256 none CC1=NNC(C)=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 87, 87, 87, 48, 48, 48, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 48, 201, 201, 201, 201, 201, 201, 201, 201, 201, 87, 48, 48, 48, 48, 12, 6, 6, 4, 4, 48, 48] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 752 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113256 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113256 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113256/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113256/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113256 Building REAL300020113257 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113257' /scratch/stefan/7770410/working/building/REAL300020113257 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113257 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113257/0 /scratch/stefan/7770410/working/building/REAL300020113257 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/111 `/scratch/stefan/7770410/working/3D/111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1) `REAL300020113257.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113257 none CCC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 28, 28, 43, 43, 28, 22, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 18, 29, 29, 29, 29, 29, 7, 7, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43, 28, 28, 22, 22, 5, 1, 1, 1, 1, 7, 18, 18, 29, 29, 1, 1, 43, 43] 201 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 44, 50, 51, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 396 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113257 none CCC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [134, 117, 117, 134, 134, 117, 96, 16, 16, 16, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 134, 134, 134, 134, 134, 134, 134, 134, 134, 117, 117, 96, 96, 16, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 134, 134] 201 rigid atoms, others: [45, 14, 13, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 661 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113257 none CCC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 7, 25, 25, 25, 43, 43, 43, 134, 134, 134, 169, 201, 201, 201, 201, 201, 134, 134, 43, 1, 1, 2, 2, 2, 1, 1, 1, 1, 3, 3, 7, 7, 25, 43, 43, 43, 43, 134, 169, 169, 201, 201, 43, 43, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 32, 5, 6, 33, 34, 35, 52, 53, 4, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 659 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113257 none CCC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 192, 192, 201, 201, 192, 172, 42, 42, 42, 30, 30, 30, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 30, 201, 201, 201, 201, 201, 201, 201, 201, 201, 192, 192, 172, 172, 42, 30, 30, 30, 30, 7, 4, 4, 2, 2, 30, 30, 201, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 818 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113257 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113257/1 /scratch/stefan/7770410/working/building/REAL300020113257 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 112) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/112 `/scratch/stefan/7770410/working/3D/112' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1) `REAL300020113257.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113257 none CCC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 28, 28, 43, 43, 28, 22, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 18, 29, 29, 29, 29, 29, 7, 7, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43, 28, 28, 22, 22, 5, 1, 1, 1, 1, 7, 18, 18, 29, 29, 1, 1, 43, 43] 201 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 44, 50, 51, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 396 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113257 none CCC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [137, 119, 119, 137, 137, 119, 97, 16, 16, 16, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 137, 137, 137, 137, 137, 137, 137, 137, 137, 119, 119, 97, 97, 16, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 137, 137] 201 rigid atoms, others: [45, 14, 13, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 681 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113257 none CCC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 7, 25, 25, 25, 43, 43, 43, 137, 137, 137, 170, 201, 201, 201, 201, 201, 137, 137, 43, 1, 1, 2, 2, 2, 1, 1, 1, 1, 3, 3, 7, 7, 25, 43, 43, 43, 43, 137, 170, 170, 201, 201, 43, 43, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 32, 5, 6, 33, 34, 35, 52, 53, 4, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 644 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113257 none CCC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 191, 191, 201, 201, 191, 170, 41, 41, 41, 29, 29, 29, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 29, 201, 201, 201, 201, 201, 201, 201, 201, 201, 191, 191, 170, 170, 41, 29, 29, 29, 29, 7, 4, 4, 2, 2, 29, 29, 201, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 827 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113257 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113257 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113257/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113257/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113257 Building REAL300020113258 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113258' /scratch/stefan/7770410/working/building/REAL300020113258 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113258 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113258/0 /scratch/stefan/7770410/working/building/REAL300020113258 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/113 `/scratch/stefan/7770410/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)NCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113258.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113258 none CC(C)(C)C(=O)NCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 118, 118, 118, 113, 23, 23, 23, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 113, 113, 23, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [44, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 438 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113258 none CC(C)(C)C(=O)NCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 75, 75, 75, 37, 37, 37, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 37, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 75, 37, 37, 37, 37, 8, 4, 4, 2, 2, 37, 37] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 727 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113258 none CC(C)(C)C(=O)NCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 38, 38, 38, 30, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 25, 37, 37, 37, 37, 37, 8, 8, 1, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 30, 30, 5, 1, 1, 1, 1, 8, 25, 25, 37, 37, 1, 1] 201 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 49, 50, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113258 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113258/1 /scratch/stefan/7770410/working/building/REAL300020113258 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 114) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/114 `/scratch/stefan/7770410/working/3D/114' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)NCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113258.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113258 none CC(C)(C)C(=O)NCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 120, 120, 120, 120, 115, 23, 23, 23, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 120, 120, 120, 120, 120, 120, 120, 120, 120, 120, 115, 115, 23, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [44, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 444 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113258 none CC(C)(C)C(=O)NCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 76, 76, 76, 38, 38, 38, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 38, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 76, 38, 38, 38, 38, 9, 4, 4, 2, 2, 38, 38] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 721 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113258 none CC(C)(C)C(=O)NCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 38, 38, 38, 30, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 25, 37, 37, 37, 37, 37, 8, 8, 1, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 30, 30, 5, 1, 1, 1, 1, 8, 25, 25, 37, 37, 1, 1] 201 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 49, 50, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113258 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113258 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113258/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113258/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113258 Building REAL300020113259 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113259' /scratch/stefan/7770410/working/building/REAL300020113259 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113259 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113259/0 /scratch/stefan/7770410/working/building/REAL300020113259 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/115 `/scratch/stefan/7770410/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NOC(C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113259.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113259 none CCC1=NOC(C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 20, 20, 20, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 20, 31, 31, 31, 31, 31, 8, 8, 1, 34, 34, 34, 34, 34, 20, 20, 20, 6, 1, 1, 1, 1, 8, 20, 20, 31, 31, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 243 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113259 none CCC1=NOC(C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [121, 88, 88, 88, 88, 88, 88, 21, 21, 21, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 121, 121, 121, 121, 121, 88, 88, 88, 21, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 363 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113259 none CCC1=NOC(C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 20, 20, 20, 88, 88, 88, 131, 176, 176, 176, 176, 176, 88, 88, 20, 5, 5, 5, 5, 5, 2, 2, 2, 8, 20, 20, 20, 20, 88, 131, 131, 176, 176, 20, 20] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 655 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113259 none CCC1=NOC(C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 176, 176, 176, 176, 176, 176, 52, 52, 52, 32, 32, 32, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 32, 201, 201, 201, 201, 201, 176, 176, 176, 52, 32, 32, 32, 32, 8, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 461 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113259 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113259/1 /scratch/stefan/7770410/working/building/REAL300020113259 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 116) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/116 `/scratch/stefan/7770410/working/3D/116' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NOC(C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113259.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113259 none CCC1=NOC(C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 20, 20, 20, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 20, 31, 31, 31, 31, 31, 8, 8, 1, 34, 34, 34, 34, 34, 20, 20, 20, 6, 1, 1, 1, 1, 8, 20, 20, 31, 31, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 243 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113259 none CCC1=NOC(C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [121, 88, 88, 88, 88, 88, 88, 21, 21, 21, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 121, 121, 121, 121, 121, 88, 88, 88, 21, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 363 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113259 none CCC1=NOC(C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 20, 20, 20, 88, 88, 88, 132, 176, 176, 176, 176, 176, 88, 88, 20, 5, 5, 5, 5, 5, 2, 2, 2, 8, 20, 20, 20, 20, 88, 132, 132, 176, 176, 20, 20] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 655 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113259 none CCC1=NOC(C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 176, 176, 176, 176, 176, 176, 52, 52, 52, 32, 32, 32, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 32, 201, 201, 201, 201, 201, 176, 176, 176, 52, 32, 32, 32, 32, 8, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 460 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113259 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113259 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113259/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113259/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113259 Building REAL300020113260 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113260' /scratch/stefan/7770410/working/building/REAL300020113260 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113260 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113260/0 /scratch/stefan/7770410/working/building/REAL300020113260 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/117 `/scratch/stefan/7770410/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2OCCOC2=C1) `REAL300020113260.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113260 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2OCCOC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 26, 74, 74, 74, 74, 74, 74, 74, 74, 74, 26, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 74, 74, 74, 74, 74, 74, 74] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 171 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113260 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2OCCOC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 48, 48, 48, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 48, 82, 201, 201, 201, 201, 201, 201, 201, 201, 201, 82, 48, 48, 48, 48, 11, 6, 6, 4, 4, 48, 48, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 411 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113260 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2OCCOC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 29, 43, 47, 47, 47, 47, 9, 9, 1, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 9, 29, 29, 43, 43, 1, 1, 14, 14, 14, 14, 14, 14, 14] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113260 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2OCCOC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 14, 14, 14, 74, 74, 74, 148, 201, 201, 201, 201, 201, 74, 74, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 14, 14, 14, 14, 74, 148, 148, 201, 201, 14, 14, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 47, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 811 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113260 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113260/1 /scratch/stefan/7770410/working/building/REAL300020113260 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 118) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/118 `/scratch/stefan/7770410/working/3D/118' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2OCCOC2=C1) `REAL300020113260.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113260 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2OCCOC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 26, 73, 73, 73, 73, 73, 73, 73, 73, 73, 26, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 73, 73, 73, 73, 73, 73, 73] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 169 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113260 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2OCCOC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 49, 49, 49, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 49, 83, 201, 201, 201, 201, 201, 201, 201, 201, 201, 83, 49, 49, 49, 49, 11, 6, 6, 4, 4, 49, 49, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 412 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113260 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2OCCOC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 30, 44, 48, 48, 48, 48, 9, 9, 1, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 9, 30, 30, 44, 44, 1, 1, 13, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113260 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2OCCOC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 13, 13, 13, 73, 73, 73, 147, 201, 201, 201, 201, 201, 73, 73, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 13, 73, 147, 147, 201, 201, 13, 13, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 47, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 812 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113260 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113260 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113260/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113260/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113260 Building REAL300020113261 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113261' /scratch/stefan/7770410/working/building/REAL300020113261 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113261 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113261/0 /scratch/stefan/7770410/working/building/REAL300020113261 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/119 `/scratch/stefan/7770410/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN=C1) `REAL300020113261.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113261 none CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 58, 19, 19, 19, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 75, 122, 122, 122, 122, 122, 75, 75, 75, 75, 58, 58, 19, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8, 122, 122, 122, 122] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 415 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113261 none CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [132, 113, 49, 49, 49, 32, 32, 32, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 32, 132, 201, 201, 201, 201, 201, 132, 132, 132, 132, 113, 113, 49, 32, 32, 32, 32, 7, 4, 4, 2, 2, 32, 32, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 667 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113261 none CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 16, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 21, 32, 32, 32, 32, 32, 8, 8, 1, 22, 32, 32, 32, 32, 32, 22, 22, 22, 22, 16, 16, 5, 1, 1, 1, 1, 8, 21, 21, 32, 32, 1, 1, 32, 32, 32, 32] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 44, 45, 21, 38, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47, 48, 49]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113261 none CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 7, 18, 18, 18, 32, 32, 32, 122, 122, 122, 170, 201, 201, 201, 201, 201, 122, 122, 32, 1, 1, 1, 1, 1, 1, 3, 3, 3, 2, 7, 7, 18, 32, 32, 32, 32, 122, 170, 170, 201, 201, 32, 32, 1, 1, 1, 1] 201 rigid atoms, others: [1, 46, 47, 48, 49, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 678 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113261 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113261/1 /scratch/stefan/7770410/working/building/REAL300020113261 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 120) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/120 `/scratch/stefan/7770410/working/3D/120' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN=C1) `REAL300020113261.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113261/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113261 none CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 57, 19, 19, 19, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 74, 122, 122, 122, 122, 122, 74, 74, 74, 74, 57, 57, 19, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8, 122, 122, 122, 122] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 414 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113261 none CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [132, 112, 49, 49, 49, 32, 32, 32, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 32, 132, 201, 201, 201, 201, 201, 132, 132, 132, 132, 112, 112, 49, 32, 32, 32, 32, 7, 4, 4, 2, 2, 32, 32, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 673 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113261 none CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 16, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 21, 32, 32, 32, 32, 32, 8, 8, 1, 22, 33, 33, 33, 33, 33, 22, 22, 22, 22, 16, 16, 5, 1, 1, 1, 1, 8, 21, 21, 32, 32, 1, 1, 33, 33, 33, 33] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 44, 45, 21, 38, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47, 48, 49]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113261 none CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 7, 18, 18, 18, 33, 33, 33, 122, 122, 122, 170, 201, 201, 201, 201, 201, 122, 122, 33, 1, 1, 1, 1, 1, 1, 3, 3, 3, 2, 7, 7, 18, 33, 33, 33, 33, 122, 170, 170, 201, 201, 33, 33, 1, 1, 1, 1] 201 rigid atoms, others: [1, 46, 47, 48, 49, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 681 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113261 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113261 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113261/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113261/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113261 Building REAL300020113262 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113262' /scratch/stefan/7770410/working/building/REAL300020113262 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113262 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113262/0 /scratch/stefan/7770410/working/building/REAL300020113262 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/121 `/scratch/stefan/7770410/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1) `REAL300020113262.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113262 none CC1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 45, 49, 49, 49, 49, 11, 11, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 11, 31, 31, 45, 45, 1, 1, 18, 18] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 44, 45, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47]) total number of confs: 230 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113262 none CC1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 81, 31, 31, 31, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 31, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 81, 81] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 243 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113262 none CC1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 18, 18, 18, 81, 81, 81, 154, 201, 201, 201, 201, 201, 81, 81, 18, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 8, 18, 18, 18, 18, 81, 154, 154, 201, 201, 18, 18, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 46, 47, 24, 33, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 791 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113262 none CC1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 93, 93, 93, 50, 50, 50, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 50, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 93, 50, 50, 50, 50, 11, 6, 6, 4, 4, 50, 50, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 589 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113262 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113262/1 /scratch/stefan/7770410/working/building/REAL300020113262 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 122) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/122 `/scratch/stefan/7770410/working/3D/122' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1) `REAL300020113262.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113262 none CC1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 45, 49, 49, 49, 49, 11, 11, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 11, 31, 31, 45, 45, 1, 1, 18, 18] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 44, 45, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47]) total number of confs: 230 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113262 none CC1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 81, 31, 31, 31, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 31, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 81, 81] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 243 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113262 none CC1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 18, 18, 18, 81, 81, 81, 154, 201, 201, 201, 201, 201, 81, 81, 18, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 8, 18, 18, 18, 18, 81, 154, 154, 201, 201, 18, 18, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 46, 47, 24, 33, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 788 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113262 none CC1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 92, 92, 92, 49, 49, 49, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 49, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 92, 49, 49, 49, 49, 10, 6, 6, 4, 4, 49, 49, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 589 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113262 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113262 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113262/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113262/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113262 Building REAL300020113263 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113263' /scratch/stefan/7770410/working/building/REAL300020113263 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113263 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113263/0 /scratch/stefan/7770410/working/building/REAL300020113263 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/123 `/scratch/stefan/7770410/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C(C)C)=N1) `REAL300020113263.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113263 none CC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 11, 18, 18, 18, 18, 18, 5, 5, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 5, 11, 11, 18, 18, 1, 1, 18, 18, 18, 18, 18, 18, 18] 66 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 180 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113263 none CC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 41, 41, 17, 17, 17, 5, 5, 5, 1, 1, 1, 1, 1, 4, 6, 6, 6, 6, 6, 1, 1, 5, 41, 41, 41, 41, 41, 41, 41, 41, 41, 17, 5, 5, 5, 5, 1, 4, 4, 6, 6, 5, 5, 41, 41, 41, 41, 41, 41, 41] 66 rigid atoms, others: [38, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 247 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113263 none CC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 18, 18, 18, 41, 41, 41, 53, 66, 66, 66, 66, 66, 41, 41, 18, 1, 1, 2, 2, 1, 2, 2, 2, 1, 8, 18, 18, 18, 18, 41, 53, 53, 66, 66, 18, 18, 2, 2, 2, 2, 2, 2, 2] 66 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 24, 25, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113263 none CC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 66, 66, 33, 33, 33, 18, 18, 18, 6, 6, 6, 4, 2, 1, 1, 1, 1, 1, 1, 6, 6, 18, 66, 66, 66, 66, 66, 66, 66, 66, 66, 33, 18, 18, 18, 18, 6, 4, 4, 2, 2, 18, 18, 66, 66, 66, 66, 66, 66, 66] 66 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 358 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113263 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113263/1 /scratch/stefan/7770410/working/building/REAL300020113263 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 124) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/124 `/scratch/stefan/7770410/working/3D/124' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C(C)C)=N1) `REAL300020113263.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113263/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113263 none CC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 11, 18, 18, 18, 18, 18, 5, 5, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 5, 11, 11, 18, 18, 1, 1, 18, 18, 18, 18, 18, 18, 18] 65 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 180 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113263 none CC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 41, 41, 17, 17, 17, 5, 5, 5, 1, 1, 1, 1, 1, 4, 6, 6, 6, 6, 6, 1, 1, 5, 41, 41, 41, 41, 41, 41, 41, 41, 41, 17, 5, 5, 5, 5, 1, 4, 4, 6, 6, 5, 5, 41, 41, 41, 41, 41, 41, 41] 65 rigid atoms, others: [38, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 247 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113263 none CC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 18, 18, 18, 41, 41, 41, 52, 65, 65, 65, 65, 65, 41, 41, 18, 1, 1, 2, 2, 1, 2, 2, 2, 1, 8, 18, 18, 18, 18, 41, 52, 52, 65, 65, 18, 18, 2, 2, 2, 2, 2, 2, 2] 65 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 24, 25, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113263 none CC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 65, 65, 33, 33, 33, 18, 18, 18, 6, 6, 6, 4, 2, 1, 1, 1, 1, 1, 1, 6, 6, 18, 65, 65, 65, 65, 65, 65, 65, 65, 65, 33, 18, 18, 18, 18, 6, 4, 4, 2, 2, 18, 18, 65, 65, 65, 65, 65, 65, 65] 65 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 353 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113263 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113263 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113263/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113263/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113263 Building REAL300020113264 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113264' /scratch/stefan/7770410/working/building/REAL300020113264 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113264 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113264/0 /scratch/stefan/7770410/working/building/REAL300020113264 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/125 `/scratch/stefan/7770410/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC(C)=C1) `REAL300020113264.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113264 none COC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 36, 51, 54, 54, 54, 54, 11, 11, 1, 15, 15, 15, 15, 21, 21, 21, 6, 1, 1, 1, 1, 11, 36, 36, 51, 51, 1, 1, 15, 15, 15, 15] 201 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 40, 22, 41, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 42, 43, 44, 45]) total number of confs: 246 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113264 none COC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 81, 81, 38, 38, 38, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 81, 81, 81, 81, 97, 97, 97, 38, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 81, 81, 81, 81] 201 rigid atoms, others: [35, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 230 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113264 none COC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 81, 81, 81, 155, 201, 201, 201, 201, 201, 81, 81, 15, 1, 1, 1, 1, 4, 4, 4, 5, 15, 15, 15, 15, 81, 155, 155, 201, 201, 15, 15, 2, 2, 2, 1] 201 rigid atoms, others: [1, 2, 3, 4, 45, 23, 24, 25, 26] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 762 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113264 none COC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 104, 104, 104, 55, 55, 55, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 55, 201, 201, 201, 201, 201, 201, 201, 104, 55, 55, 55, 55, 13, 6, 6, 4, 4, 55, 55, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 437 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113264 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113264/1 /scratch/stefan/7770410/working/building/REAL300020113264 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 126) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/126 `/scratch/stefan/7770410/working/3D/126' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC(C)=C1) `REAL300020113264.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113264/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113264 none COC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 35, 50, 53, 53, 53, 53, 11, 11, 1, 15, 15, 15, 15, 21, 21, 21, 6, 1, 1, 1, 1, 11, 35, 35, 50, 50, 1, 1, 15, 15, 15, 15] 201 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 40, 22, 41, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 42, 43, 44, 45]) total number of confs: 240 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113264 none COC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 80, 80, 37, 37, 37, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 80, 80, 80, 80, 97, 97, 97, 37, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 80, 80, 80, 80] 201 rigid atoms, others: [35, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 228 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113264 none COC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 80, 80, 80, 154, 201, 201, 201, 201, 201, 80, 80, 15, 1, 1, 1, 1, 4, 4, 4, 5, 15, 15, 15, 15, 80, 154, 154, 201, 201, 15, 15, 2, 2, 2, 1] 201 rigid atoms, others: [1, 2, 3, 4, 45, 23, 24, 25, 26] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 767 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113264 none COC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 104, 104, 104, 55, 55, 55, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 55, 201, 201, 201, 201, 201, 201, 201, 104, 55, 55, 55, 55, 13, 6, 6, 4, 4, 55, 55, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 436 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113264 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113264 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113264/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113264/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113264 Building REAL300020113265 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113265' /scratch/stefan/7770410/working/building/REAL300020113265 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300020113265 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113265/0 /scratch/stefan/7770410/working/building/REAL300020113265 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/127 `/scratch/stefan/7770410/working/3D/127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[NH+]1CCCCCC1) `REAL300020113265.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113265 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[NH+]1CCCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 9, 6, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [27, 22, 22, 22, 9, 9, 9, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 22, 9, 9, 9, 9, 1, 4, 4, 4, 4, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27] 28 rigid atoms, others: [38, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 99 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113265 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[NH+]1CCCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 9, 6, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 23, 23, 23, 10, 10, 10, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 23, 10, 10, 10, 10, 4, 3, 3, 1, 1, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 28 rigid atoms, others: [41, 42, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 96 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113265 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[NH+]1CCCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 9, 6, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 10, 10, 10, 10, 10, 10, 9, 9, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 9, 10, 10, 10, 10, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 28 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 43, 44, 20, 36, 37] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 52 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113265 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[NH+]1CCCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 9, 6, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 5, 5, 11, 11, 11, 27, 27, 27, 28, 28, 28, 28, 28, 28, 27, 27, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 11, 11, 11, 11, 27, 28, 28, 28, 28, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 28 rigid atoms, others: [1, 56, 54, 55, 45, 46, 47, 48, 49, 50, 51, 52, 21, 22, 23, 24, 25, 26, 27, 28, 53] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 61 number of broken/clashed sets: 3 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113265 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113265 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 0: /scratch/stefan/7770410/working/building/REAL300020113265/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113265 Building REAL300020113266 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113266' /scratch/stefan/7770410/working/building/REAL300020113266 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113266 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113266/0 /scratch/stefan/7770410/working/building/REAL300020113266 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/128 `/scratch/stefan/7770410/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NOC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020113266.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113266 none CC(C)C1=NOC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 14, 26, 14, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 39, 57, 68, 68, 68, 68, 13, 13, 1, 14, 26, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 13, 39, 39, 57, 57, 1, 1, 14] 201 rigid atoms, others: [45, 35, 36, 37, 38, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46]) total number of confs: 333 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113266 none CC(C)C1=NOC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [121, 82, 121, 82, 82, 82, 55, 55, 55, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 82, 121, 121, 121, 121, 121, 121, 121, 55, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 82] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 427 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113266 none CC(C)C1=NOC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 82, 82, 82, 146, 176, 188, 188, 188, 188, 82, 82, 14, 1, 5, 5, 5, 5, 5, 5, 5, 6, 14, 14, 14, 14, 82, 146, 146, 176, 176, 14, 14, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 46, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 630 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113266 none CC(C)C1=NOC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 188, 201, 188, 188, 188, 182, 182, 182, 73, 73, 73, 12, 12, 12, 7, 4, 1, 1, 1, 1, 1, 1, 12, 12, 73, 188, 201, 201, 201, 201, 201, 201, 201, 182, 73, 73, 73, 73, 12, 7, 7, 4, 4, 73, 73, 188] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 603 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113266 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113266/1 /scratch/stefan/7770410/working/building/REAL300020113266 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 129) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/129 `/scratch/stefan/7770410/working/3D/129' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NOC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020113266.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113266/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113266 none CC(C)C1=NOC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 14, 27, 14, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 39, 57, 68, 68, 68, 68, 13, 13, 1, 14, 27, 27, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 13, 39, 39, 57, 57, 1, 1, 14] 201 rigid atoms, others: [45, 35, 36, 37, 38, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46]) total number of confs: 336 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113266 none CC(C)C1=NOC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [122, 82, 122, 82, 82, 82, 55, 55, 55, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 82, 122, 122, 122, 122, 122, 122, 122, 55, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 82] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 429 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113266 none CC(C)C1=NOC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 82, 82, 82, 145, 176, 188, 188, 188, 188, 82, 82, 14, 1, 5, 5, 5, 5, 5, 5, 5, 6, 14, 14, 14, 14, 82, 145, 145, 176, 176, 14, 14, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 46, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 634 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113266 none CC(C)C1=NOC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 187, 201, 187, 187, 187, 181, 181, 181, 72, 72, 72, 12, 12, 12, 7, 4, 1, 1, 1, 1, 1, 1, 12, 12, 72, 187, 201, 201, 201, 201, 201, 201, 201, 181, 72, 72, 72, 72, 12, 7, 7, 4, 4, 72, 72, 187] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 607 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113266 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113266 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113266/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113266/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113266 Building REAL300020113267 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113267' /scratch/stefan/7770410/working/building/REAL300020113267 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113267 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113267/0 /scratch/stefan/7770410/working/building/REAL300020113267 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/130 `/scratch/stefan/7770410/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[N@@H+]1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113267.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113267 none CC(C)[N@@H+]1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 9, 8, 8, 8, 8, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 9, 9, 9, 9, 9, 9, 8, 8, 1, 9, 9, 9, 9, 9, 9, 9, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 1, 1, 1, 1, 8, 9, 9, 9, 9, 1, 1] 29 rigid atoms, others: [16, 12, 13, 46, 15, 48, 49, 14, 55, 56, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53, 54]) total number of confs: 41 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113267 none CC(C)[N@@H+]1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 29, 29, 23, 23, 23, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 23, 8, 8, 8, 8, 1, 3, 3, 3, 3, 8, 8] 29 rigid atoms, others: [50, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56]) total number of confs: 92 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113267 none CC(C)[N@@H+]1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 8, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 29, 29, 29, 29, 29, 8, 8] 29 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 42, 39, 44, 40, 43, 41, 36, 38, 10, 37] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 56 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113267 none CC(C)[N@@H+]1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 29, 29, 23, 23, 23, 10, 10, 10, 4, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 4, 4, 10, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 23, 10, 10, 10, 10, 4, 4, 4, 2, 2, 10, 10] 29 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 94 number of broken/clashed sets: 5 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113267 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113267/1 /scratch/stefan/7770410/working/building/REAL300020113267 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 131) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/131 `/scratch/stefan/7770410/working/3D/131' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[N@H+]1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113267.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113267/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113267 none CC(C)[N@H+]1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 10, 10, 10, 10, 10, 10, 9, 9, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 1, 1, 1, 9, 10, 10, 10, 10, 1, 1] 28 rigid atoms, others: [16, 12, 13, 46, 15, 48, 49, 14, 55, 56, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53, 54]) total number of confs: 32 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113267 none CC(C)[N@H+]1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 28, 21, 21, 21, 9, 9, 9, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 21, 9, 9, 9, 9, 1, 3, 3, 3, 3, 9, 9] 28 rigid atoms, others: [50, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56]) total number of confs: 90 number of broken/clashed sets: 28 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113267 none CC(C)[N@H+]1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 7, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 28, 28, 28, 28, 28, 7, 7] 28 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 42, 39, 44, 40, 43, 41, 36, 38, 10, 37] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 54 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113267 none CC(C)[N@H+]1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 28, 21, 21, 21, 10, 10, 10, 4, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 4, 4, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 21, 10, 10, 10, 10, 4, 4, 4, 2, 2, 10, 10] 28 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 90 number of broken/clashed sets: 28 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113267 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113267 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113267/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113267/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113267 Building REAL300020113268 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113268' /scratch/stefan/7770410/working/building/REAL300020113268 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113268 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113268/0 /scratch/stefan/7770410/working/building/REAL300020113268 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/132 `/scratch/stefan/7770410/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1) `REAL300020113268.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113268 none CCN1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 8, 8, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 40, 58, 71, 71, 71, 71, 12, 12, 1, 8, 17, 17, 17, 17, 17, 8, 8, 6, 1, 1, 1, 1, 12, 40, 40, 58, 58, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 325 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113268 none CCN1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 49, 49, 49, 49, 46, 46, 46, 12, 12, 12, 1, 1, 1, 1, 1, 6, 8, 11, 11, 11, 11, 1, 1, 12, 49, 95, 95, 95, 95, 95, 49, 49, 46, 12, 12, 12, 12, 1, 6, 6, 8, 8, 12, 12] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 425 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113268 none CCN1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 49, 49, 49, 115, 143, 154, 154, 154, 154, 49, 49, 8, 1, 5, 5, 5, 5, 5, 1, 1, 4, 8, 8, 8, 8, 49, 115, 115, 143, 143, 8, 8] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 25, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 577 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113268 none CCN1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 154, 154, 154, 154, 154, 154, 154, 71, 71, 71, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 71, 154, 201, 201, 201, 201, 201, 154, 154, 154, 71, 71, 71, 71, 11, 6, 6, 4, 4, 71, 71] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 719 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113268 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113268/1 /scratch/stefan/7770410/working/building/REAL300020113268 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 133) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/133 `/scratch/stefan/7770410/working/3D/133' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1) `REAL300020113268.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113268/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113268 none CCN1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 8, 8, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 40, 58, 71, 71, 71, 71, 12, 12, 1, 8, 17, 17, 17, 17, 17, 8, 8, 6, 1, 1, 1, 1, 12, 40, 40, 58, 58, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 325 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113268 none CCN1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 48, 48, 48, 48, 46, 46, 46, 12, 12, 12, 1, 1, 1, 1, 1, 6, 8, 11, 11, 11, 11, 1, 1, 12, 48, 93, 93, 93, 93, 93, 48, 48, 46, 12, 12, 12, 12, 1, 6, 6, 8, 8, 12, 12] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 417 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113268 none CCN1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 48, 48, 48, 115, 144, 155, 155, 155, 155, 48, 48, 8, 1, 5, 5, 5, 5, 5, 1, 1, 4, 8, 8, 8, 8, 48, 115, 115, 144, 144, 8, 8] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 25, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 587 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113268 none CCN1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 158, 158, 158, 158, 158, 158, 158, 72, 72, 72, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 72, 158, 201, 201, 201, 201, 201, 158, 158, 158, 72, 72, 72, 72, 11, 6, 6, 4, 4, 72, 72] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 705 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113268 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113268 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113268/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113268/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113268 Building REAL300020113269 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113269' /scratch/stefan/7770410/working/building/REAL300020113269 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113269 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113269/0 /scratch/stefan/7770410/working/building/REAL300020113269 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/134 `/scratch/stefan/7770410/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)N1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1) `REAL300020113269.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113269 none CCC(CC)N1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 13, 8, 13, 15, 8, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 44, 62, 71, 71, 71, 71, 13, 13, 1, 8, 15, 15, 15, 15, 15, 13, 15, 15, 15, 15, 15, 8, 8, 6, 1, 1, 1, 1, 13, 44, 44, 62, 62, 1, 1] 201 rigid atoms, others: [11, 15, 44, 43, 12, 13, 14, 45, 52, 46, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 333 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113269 none CCC(CC)N1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 92, 57, 92, 94, 57, 57, 57, 51, 51, 51, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 13, 57, 94, 94, 94, 94, 94, 92, 94, 94, 94, 94, 94, 57, 57, 51, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13] 201 rigid atoms, others: [14, 47, 16, 17, 18, 25, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 411 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113269 none CCC(CC)N1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 3, 1, 3, 4, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 57, 57, 57, 139, 187, 197, 197, 197, 197, 57, 57, 8, 1, 4, 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 1, 1, 3, 8, 8, 8, 8, 57, 139, 139, 187, 187, 8, 8] 201 rigid atoms, others: [2, 5, 6, 7, 40, 41, 8, 9, 28] set([0, 1, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 782 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113269 none CCC(CC)N1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 197, 199, 201, 197, 197, 197, 192, 192, 192, 71, 71, 71, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 71, 197, 201, 201, 201, 201, 201, 199, 201, 201, 201, 201, 201, 197, 197, 192, 71, 71, 71, 71, 12, 6, 6, 4, 4, 71, 71] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 560 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113269 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113269/1 /scratch/stefan/7770410/working/building/REAL300020113269 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 135) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/135 `/scratch/stefan/7770410/working/3D/135' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)N1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1) `REAL300020113269.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113269/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113269 none CCC(CC)N1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 13, 8, 13, 15, 8, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 45, 63, 71, 71, 71, 71, 13, 13, 1, 8, 15, 15, 15, 15, 15, 13, 15, 15, 15, 15, 15, 8, 8, 6, 1, 1, 1, 1, 13, 45, 45, 63, 63, 1, 1] 201 rigid atoms, others: [11, 15, 44, 43, 12, 13, 14, 45, 52, 46, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 334 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113269 none CCC(CC)N1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 90, 56, 90, 92, 56, 56, 56, 51, 51, 51, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 13, 56, 92, 92, 92, 92, 92, 90, 92, 92, 92, 92, 92, 56, 56, 51, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13] 201 rigid atoms, others: [14, 47, 16, 17, 18, 25, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 403 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113269 none CCC(CC)N1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 3, 1, 3, 4, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 56, 56, 56, 140, 188, 197, 197, 197, 197, 56, 56, 8, 1, 4, 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 1, 1, 3, 8, 8, 8, 8, 56, 140, 140, 188, 188, 8, 8] 201 rigid atoms, others: [2, 5, 6, 7, 40, 41, 8, 9, 28] set([0, 1, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 785 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113269 none CCC(CC)N1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 197, 199, 201, 197, 197, 197, 192, 192, 192, 70, 70, 70, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 70, 197, 201, 201, 201, 201, 201, 199, 201, 201, 201, 201, 201, 197, 197, 192, 70, 70, 70, 70, 12, 6, 6, 4, 4, 70, 70] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 560 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113269 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113269 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113269/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113269/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113269 Building REAL300020113270 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113270' /scratch/stefan/7770410/working/building/REAL300020113270 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113270 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113270/0 /scratch/stefan/7770410/working/building/REAL300020113270 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/136 `/scratch/stefan/7770410/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@@](C)(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1(C)C) `REAL300020113270.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113270 none C[C@H]1CC[C@@](C)(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 14, 6, 14, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 46, 64, 79, 79, 79, 79, 11, 11, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 11, 46, 46, 64, 64, 1, 1, 14, 14, 14, 14, 14, 14] 201 rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 49, 50, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 51, 52, 53, 54, 55, 56]) total number of confs: 323 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113270 none C[C@H]1CC[C@@](C)(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 91, 91, 47, 91, 47, 47, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 14, 14, 14, 14, 1, 1, 11, 91, 91, 91, 91, 91, 91, 91, 91, 91, 91, 91, 91, 91, 47, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 91, 91, 91, 91, 91, 91] 201 rigid atoms, others: [12, 44, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 311 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113270 none C[C@H]1CC[C@@](C)(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 91, 91, 91, 161, 201, 201, 201, 201, 201, 91, 91, 14, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 14, 14, 14, 14, 91, 161, 161, 201, 201, 14, 14, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 34, 35, 26, 27, 28, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 755 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113270 none C[C@H]1CC[C@@](C)(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 143, 201, 143, 143, 79, 79, 79, 16, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 79, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 143, 79, 79, 79, 79, 16, 6, 6, 4, 4, 79, 79, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 608 number of broken/clashed sets: 200 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113270 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113270/1 /scratch/stefan/7770410/working/building/REAL300020113270 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 137) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/137 `/scratch/stefan/7770410/working/3D/137' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@@](C)(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1(C)C) `REAL300020113270.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113270 none C[C@H]1CC[C@@](C)(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 14, 6, 14, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 47, 65, 81, 81, 81, 81, 11, 11, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 11, 47, 47, 65, 65, 1, 1, 14, 14, 14, 14, 14, 14] 201 rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 49, 50, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 51, 52, 53, 54, 55, 56]) total number of confs: 328 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113270 none C[C@H]1CC[C@@](C)(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 90, 90, 47, 90, 47, 47, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 14, 14, 14, 14, 1, 1, 11, 90, 90, 90, 90, 90, 90, 90, 90, 90, 90, 90, 90, 90, 47, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 90, 90, 90, 90, 90, 90] 201 rigid atoms, others: [12, 44, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 307 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113270 none C[C@H]1CC[C@@](C)(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 90, 90, 90, 161, 201, 201, 201, 201, 201, 90, 90, 14, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 14, 14, 14, 14, 90, 161, 161, 201, 201, 14, 14, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 34, 35, 26, 27, 28, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 760 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113270 none C[C@H]1CC[C@@](C)(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 144, 201, 144, 144, 81, 81, 81, 16, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 81, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 144, 81, 81, 81, 81, 16, 6, 6, 4, 4, 81, 81, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 604 number of broken/clashed sets: 200 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113270 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113270 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113270/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113270/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113270 Building REAL300020113271 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113271' /scratch/stefan/7770410/working/building/REAL300020113271 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113271 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113271/0 /scratch/stefan/7770410/working/building/REAL300020113271 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/138 `/scratch/stefan/7770410/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCCCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113271.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113271 none CC(C)CCCCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 95, 95, 112, 95, 89, 19, 19, 19, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 89, 89, 19, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [17, 13, 14, 15, 16, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55]) total number of confs: 808 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113271 none CC(C)CCCCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 177, 177, 201, 177, 193, 53, 53, 53, 32, 32, 32, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 32, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 193, 193, 53, 32, 32, 32, 32, 7, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 1242 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113271 none CC(C)CCCCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 27, 27, 31, 27, 22, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 20, 32, 32, 32, 32, 32, 7, 7, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 22, 22, 5, 1, 1, 1, 1, 7, 20, 20, 32, 32, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 46, 45, 48, 14, 54, 55, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53]) total number of confs: 338 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113271 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113271/1 /scratch/stefan/7770410/working/building/REAL300020113271 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 139) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/139 `/scratch/stefan/7770410/working/3D/139' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCCCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113271.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113271 none CC(C)CCCCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 95, 95, 112, 95, 88, 19, 19, 19, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 88, 88, 19, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [17, 13, 14, 15, 16, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55]) total number of confs: 811 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113271 none CC(C)CCCCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 178, 178, 201, 178, 192, 53, 53, 53, 32, 32, 32, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 32, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 192, 192, 53, 32, 32, 32, 32, 7, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 1224 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113271 none CC(C)CCCCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 27, 27, 31, 27, 21, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 20, 32, 32, 32, 32, 32, 7, 7, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 21, 21, 5, 1, 1, 1, 1, 7, 20, 20, 32, 32, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 46, 45, 48, 14, 54, 55, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53]) total number of confs: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113271 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113271 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113271/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113271/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113271 Building REAL300020113272 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113272' /scratch/stefan/7770410/working/building/REAL300020113272 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113272 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113272/0 /scratch/stefan/7770410/working/building/REAL300020113272 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/140 `/scratch/stefan/7770410/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(Cl)=CS1) `REAL300020113272.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113272 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(Cl)=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 16, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 8, 11, 13, 13, 13, 13, 1, 1, 5, 16, 44, 44, 44, 44, 44, 16, 5, 5, 5, 5, 1, 8, 8, 11, 11, 5, 5, 44, 44] 78 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 128 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113272 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(Cl)=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 16, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 32, 32, 32, 14, 14, 14, 7, 4, 1, 1, 1, 1, 1, 1, 14, 14, 32, 47, 79, 79, 79, 79, 79, 47, 32, 32, 32, 32, 14, 7, 7, 4, 4, 32, 32, 79, 79] 79 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 204 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113272 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(Cl)=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 16, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 19, 27, 31, 31, 31, 31, 5, 5, 1, 6, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 5, 19, 19, 27, 27, 1, 1, 24, 24] 78 rigid atoms, others: [2, 3, 4, 5, 6, 18, 35, 36, 26, 27, 28, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113272 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(Cl)=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 16, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 24, 24, 24, 44, 44, 44, 68, 78, 78, 78, 78, 78, 44, 44, 24, 1, 1, 1, 1, 1, 1, 10, 24, 24, 24, 24, 44, 68, 68, 78, 78, 24, 24, 1, 1] 78 rigid atoms, others: [1, 37, 38, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 270 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113272 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113272/1 /scratch/stefan/7770410/working/building/REAL300020113272 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 141) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/141 `/scratch/stefan/7770410/working/3D/141' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(Cl)=CS1) `REAL300020113272.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113272 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(Cl)=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 16, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 5, 16, 42, 42, 42, 42, 42, 16, 5, 5, 5, 5, 1, 8, 8, 10, 10, 5, 5, 42, 42] 75 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 120 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113272 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(Cl)=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 16, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 30, 30, 30, 13, 13, 13, 7, 4, 1, 1, 1, 1, 1, 1, 13, 13, 30, 45, 76, 76, 76, 76, 76, 45, 30, 30, 30, 30, 13, 7, 7, 4, 4, 30, 30, 76, 76] 76 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 198 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113272 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(Cl)=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 16, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 17, 25, 28, 28, 28, 28, 5, 5, 1, 6, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 5, 17, 17, 25, 25, 1, 1, 23, 23] 75 rigid atoms, others: [2, 3, 4, 5, 6, 18, 35, 36, 26, 27, 28, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113272 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(Cl)=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 16, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 23, 23, 23, 42, 42, 42, 65, 75, 75, 75, 75, 75, 42, 42, 23, 1, 1, 1, 1, 1, 1, 10, 23, 23, 23, 23, 42, 65, 65, 75, 75, 23, 23, 1, 1] 75 rigid atoms, others: [1, 37, 38, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 264 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113272 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113272 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113272/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113272/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113272 Building REAL300020113273 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113273' /scratch/stefan/7770410/working/building/REAL300020113273 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113273 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113273/0 /scratch/stefan/7770410/working/building/REAL300020113273 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/142 `/scratch/stefan/7770410/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CSC(Cl)=C1) `REAL300020113273.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113273 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CSC(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 9, 9, 9, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 9, 32, 89, 89, 89, 89, 89, 32, 9, 9, 9, 9, 1, 8, 8, 10, 10, 9, 9, 89, 89] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 206 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113273 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CSC(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 55, 55, 55, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 55, 120, 201, 201, 201, 201, 201, 120, 55, 55, 55, 55, 13, 6, 6, 4, 4, 55, 55, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 497 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113273 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CSC(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 33, 49, 54, 54, 54, 54, 9, 9, 1, 6, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 9, 33, 33, 49, 49, 1, 1, 17, 17] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 35, 36, 26, 27, 28, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113273 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CSC(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 17, 17, 17, 89, 89, 89, 162, 201, 201, 201, 201, 201, 89, 89, 17, 1, 1, 1, 1, 1, 1, 5, 17, 17, 17, 17, 89, 162, 162, 201, 201, 17, 17, 1, 1] 201 rigid atoms, others: [1, 37, 38, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 743 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113273 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113273/1 /scratch/stefan/7770410/working/building/REAL300020113273 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 143) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/143 `/scratch/stefan/7770410/working/3D/143' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CSC(Cl)=C1) `REAL300020113273.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113273/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113273 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CSC(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 32, 89, 89, 89, 89, 89, 32, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9, 89, 89] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 203 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113273 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CSC(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [122, 122, 56, 56, 56, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 56, 122, 201, 201, 201, 201, 201, 122, 56, 56, 56, 56, 13, 6, 6, 4, 4, 56, 56, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 501 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113273 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CSC(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 33, 49, 55, 55, 55, 55, 9, 9, 1, 6, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 9, 33, 33, 49, 49, 1, 1, 17, 17] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 35, 36, 26, 27, 28, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113273 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CSC(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 17, 17, 17, 89, 89, 89, 162, 201, 201, 201, 201, 201, 89, 89, 17, 1, 1, 1, 1, 1, 1, 5, 17, 17, 17, 17, 89, 162, 162, 201, 201, 17, 17, 1, 1] 201 rigid atoms, others: [1, 37, 38, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 749 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113273 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113273 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113273/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113273/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113273 Building REAL300020113274 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113274' /scratch/stefan/7770410/working/building/REAL300020113274 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113274 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113274/0 /scratch/stefan/7770410/working/building/REAL300020113274 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/144 `/scratch/stefan/7770410/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1) `REAL300020113274.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113274 none CC(CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 110, 98, 18, 18, 18, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 113, 114, 114, 113, 114, 114, 113, 113, 113, 113, 112, 112, 98, 98, 18, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 114, 114, 114, 114, 114] 201 rigid atoms, others: [9, 42, 11, 12, 13, 20, 21, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 467 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113274 none CC(CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 198, 187, 54, 54, 54, 32, 32, 32, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 32, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 200, 200, 187, 187, 54, 32, 32, 32, 32, 7, 4, 4, 2, 2, 32, 32, 201, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 765 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113274 none CC(CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 26, 22, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 20, 32, 32, 32, 32, 32, 7, 7, 1, 28, 29, 29, 28, 29, 29, 28, 28, 28, 28, 27, 27, 22, 22, 5, 1, 1, 1, 1, 7, 20, 20, 32, 32, 1, 1, 29, 29, 29, 29, 29] 201 rigid atoms, others: [6, 38, 7, 8, 9, 10, 39, 47, 48, 40, 22, 41] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50, 51, 52, 53]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113274 none CC(CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 5, 6, 15, 15, 15, 29, 29, 29, 114, 114, 114, 163, 201, 201, 201, 201, 201, 114, 114, 29, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 5, 6, 6, 15, 29, 29, 29, 29, 114, 163, 163, 201, 201, 29, 29, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 49, 50, 51, 52, 53, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 702 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113274 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113274/1 /scratch/stefan/7770410/working/building/REAL300020113274 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 145) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/145 `/scratch/stefan/7770410/working/3D/145' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1) `REAL300020113274.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113274/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113274 none CC(CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 110, 98, 18, 18, 18, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 114, 115, 115, 114, 115, 115, 114, 114, 114, 114, 112, 112, 98, 98, 18, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 115, 115, 115, 115, 115] 201 rigid atoms, others: [9, 42, 11, 12, 13, 20, 21, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 473 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113274 none CC(CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 197, 186, 54, 54, 54, 32, 32, 32, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 32, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 199, 199, 186, 186, 54, 32, 32, 32, 32, 7, 4, 4, 2, 2, 32, 32, 201, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 765 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113274 none CC(CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 26, 22, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 20, 32, 32, 32, 32, 32, 7, 7, 1, 28, 29, 29, 28, 29, 29, 28, 28, 28, 28, 27, 27, 22, 22, 5, 1, 1, 1, 1, 7, 20, 20, 32, 32, 1, 1, 29, 29, 29, 29, 29] 201 rigid atoms, others: [6, 38, 7, 8, 9, 10, 39, 47, 48, 40, 22, 41] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50, 51, 52, 53]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113274 none CC(CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 5, 6, 15, 15, 15, 29, 29, 29, 115, 115, 115, 164, 201, 201, 201, 201, 201, 115, 115, 29, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 5, 6, 6, 15, 29, 29, 29, 29, 115, 164, 164, 201, 201, 29, 29, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 49, 50, 51, 52, 53, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 698 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113274 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113274 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113274/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113274/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113274 Building REAL300020113275 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113275' /scratch/stefan/7770410/working/building/REAL300020113275 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113275 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113275/0 /scratch/stefan/7770410/working/building/REAL300020113275 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/146 `/scratch/stefan/7770410/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(Cl)SC=C1) `REAL300020113275.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113275 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(Cl)SC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 16, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 7, 7, 7, 1, 1, 1, 1, 1, 9, 15, 22, 22, 22, 22, 1, 1, 7, 26, 71, 71, 71, 71, 71, 26, 7, 7, 7, 7, 1, 9, 9, 15, 15, 7, 7, 71, 71] 149 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 206 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113275 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(Cl)SC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 16, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 68, 68, 68, 26, 26, 26, 10, 4, 1, 1, 1, 1, 1, 1, 26, 26, 68, 110, 149, 149, 149, 149, 149, 110, 68, 68, 68, 68, 26, 10, 10, 4, 4, 68, 68, 149, 149] 149 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 389 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113275 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(Cl)SC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 16, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 35, 47, 65, 65, 65, 65, 7, 7, 1, 6, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 7, 35, 35, 47, 47, 1, 1, 23, 23] 149 rigid atoms, others: [2, 3, 4, 5, 6, 18, 35, 36, 26, 27, 28, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113275 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(Cl)SC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 16, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 23, 23, 23, 71, 71, 71, 131, 149, 149, 149, 149, 149, 71, 71, 23, 1, 1, 1, 1, 1, 1, 7, 23, 23, 23, 23, 71, 131, 131, 149, 149, 23, 23, 1, 1] 149 rigid atoms, others: [1, 37, 38, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 525 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113275 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113275/1 /scratch/stefan/7770410/working/building/REAL300020113275 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 147) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/147 `/scratch/stefan/7770410/working/3D/147' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(Cl)SC=C1) `REAL300020113275.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113275 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(Cl)SC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 16, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 7, 7, 7, 1, 1, 1, 1, 1, 9, 15, 22, 22, 22, 22, 1, 1, 7, 26, 71, 71, 71, 71, 71, 26, 7, 7, 7, 7, 1, 9, 9, 15, 15, 7, 7, 71, 71] 149 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 206 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113275 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(Cl)SC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 16, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 68, 68, 68, 26, 26, 26, 10, 4, 1, 1, 1, 1, 1, 1, 26, 26, 68, 110, 149, 149, 149, 149, 149, 110, 68, 68, 68, 68, 26, 10, 10, 4, 4, 68, 68, 149, 149] 149 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 389 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113275 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(Cl)SC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 16, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 35, 47, 65, 65, 65, 65, 7, 7, 1, 6, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 7, 35, 35, 47, 47, 1, 1, 23, 23] 149 rigid atoms, others: [2, 3, 4, 5, 6, 18, 35, 36, 26, 27, 28, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113275 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(Cl)SC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 16, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 23, 23, 23, 71, 71, 71, 131, 149, 149, 149, 149, 149, 71, 71, 23, 1, 1, 1, 1, 1, 1, 7, 23, 23, 23, 23, 71, 131, 131, 149, 149, 23, 23, 1, 1] 149 rigid atoms, others: [1, 37, 38, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 525 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113275 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113275 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113275/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113275/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113275 Building REAL300020113276 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113276' /scratch/stefan/7770410/working/building/REAL300020113276 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113276 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113276/0 /scratch/stefan/7770410/working/building/REAL300020113276 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/148 `/scratch/stefan/7770410/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(NC(C)=O)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113276.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113276 none C=C(C)CC(NC(C)=O)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 8, 1, 5, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 107, 120, 80, 30, 80, 98, 98, 98, 30, 30, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 10, 120, 120, 120, 120, 120, 107, 107, 80, 98, 98, 98, 98, 30, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10] 201 rigid atoms, others: [45, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 569 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113276 none C=C(C)CC(NC(C)=O)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 8, 1, 5, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 162, 66, 162, 199, 199, 199, 66, 66, 39, 39, 39, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 39, 201, 201, 201, 201, 201, 201, 201, 162, 199, 199, 199, 199, 66, 39, 39, 39, 39, 9, 4, 4, 2, 2, 39, 39] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 976 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113276 none C=C(C)CC(NC(C)=O)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 8, 1, 5, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 31, 41, 20, 6, 20, 25, 25, 25, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 28, 42, 42, 42, 42, 42, 10, 10, 1, 41, 41, 41, 41, 41, 31, 31, 20, 25, 25, 25, 25, 6, 1, 1, 1, 1, 10, 28, 28, 42, 42, 1, 1] 201 rigid atoms, others: [43, 41, 42, 11, 12, 13, 14, 15, 50, 51, 27, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 339 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113276 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113276/1 /scratch/stefan/7770410/working/building/REAL300020113276 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 149) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/149 `/scratch/stefan/7770410/working/3D/149' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(NC(C)=O)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113276.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113276 none C=C(C)CC(NC(C)=O)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 8, 1, 5, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [121, 108, 121, 81, 30, 81, 98, 98, 98, 30, 30, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 10, 121, 121, 121, 121, 121, 108, 108, 81, 98, 98, 98, 98, 30, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10] 201 rigid atoms, others: [45, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 567 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113276 none C=C(C)CC(NC(C)=O)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 8, 1, 5, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 161, 67, 161, 199, 199, 199, 67, 67, 39, 39, 39, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 39, 201, 201, 201, 201, 201, 201, 201, 161, 199, 199, 199, 199, 67, 39, 39, 39, 39, 9, 4, 4, 2, 2, 39, 39] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 981 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113276 none C=C(C)CC(NC(C)=O)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 8, 1, 5, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 31, 41, 20, 6, 20, 24, 24, 24, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 27, 41, 41, 41, 41, 41, 10, 10, 1, 41, 41, 41, 41, 41, 31, 31, 20, 24, 24, 24, 24, 6, 1, 1, 1, 1, 10, 27, 27, 41, 41, 1, 1] 201 rigid atoms, others: [43, 41, 42, 11, 12, 13, 14, 15, 50, 51, 27, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 334 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113276 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113276 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113276/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113276/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113276 Building REAL300020113277 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113277' /scratch/stefan/7770410/working/building/REAL300020113277 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113277 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113277/0 /scratch/stefan/7770410/working/building/REAL300020113277 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/150 `/scratch/stefan/7770410/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113277.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113277 none CCCCCC(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 106, 91, 74, 91, 17, 17, 17, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 91, 91, 91, 91, 74, 74, 17, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7] 201 rigid atoms, others: [17, 13, 14, 15, 16, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55]) total number of confs: 482 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113277 none CCCCCC(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 173, 173, 138, 116, 138, 33, 33, 33, 25, 25, 25, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 25, 201, 201, 201, 201, 201, 201, 201, 173, 173, 173, 173, 138, 138, 138, 138, 116, 116, 33, 25, 25, 25, 25, 7, 4, 4, 2, 2, 25, 25] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 879 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113277 none CCCCCC(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 34, 24, 34, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 19, 30, 30, 30, 30, 30, 7, 7, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 34, 34, 34, 34, 24, 24, 5, 1, 1, 1, 1, 7, 19, 19, 30, 30, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 46, 45, 48, 14, 54, 55, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53]) total number of confs: 309 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113277 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113277/1 /scratch/stefan/7770410/working/building/REAL300020113277 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 151) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/151 `/scratch/stefan/7770410/working/3D/151' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113277.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113277 none CCCCCC(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 106, 91, 74, 91, 17, 17, 17, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 91, 91, 91, 91, 74, 74, 17, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7] 201 rigid atoms, others: [17, 13, 14, 15, 16, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55]) total number of confs: 482 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113277 none CCCCCC(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 173, 173, 138, 116, 138, 33, 33, 33, 25, 25, 25, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 25, 201, 201, 201, 201, 201, 201, 201, 173, 173, 173, 173, 138, 138, 138, 138, 116, 116, 33, 25, 25, 25, 25, 7, 4, 4, 2, 2, 25, 25] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 879 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113277 none CCCCCC(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 34, 24, 34, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 19, 30, 30, 30, 30, 30, 7, 7, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 34, 34, 34, 34, 24, 24, 5, 1, 1, 1, 1, 7, 19, 19, 30, 30, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 46, 45, 48, 14, 54, 55, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53]) total number of confs: 309 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113277 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113277 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113277/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113277/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113277 Building REAL300020113278 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113278' /scratch/stefan/7770410/working/building/REAL300020113278 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113278 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113278/0 /scratch/stefan/7770410/working/building/REAL300020113278 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/152 `/scratch/stefan/7770410/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1) `REAL300020113278.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113278 none CC1=NC=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 39, 57, 61, 61, 61, 61, 13, 13, 1, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 13, 39, 39, 57, 57, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40]) total number of confs: 260 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113278 none CC1=NC=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 91, 91, 91, 48, 48, 48, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 91, 91, 91, 91, 91, 48, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [36, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 237 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113278 none CC1=NC=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 91, 91, 91, 169, 201, 201, 201, 201, 201, 91, 91, 11, 1, 2, 2, 2, 1, 3, 11, 11, 11, 11, 91, 169, 169, 201, 201, 11, 11] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 26, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 726 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113278 none CC1=NC=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 142, 142, 142, 62, 62, 62, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 62, 201, 201, 201, 201, 201, 142, 62, 62, 62, 62, 10, 6, 6, 4, 4, 62, 62] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 517 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113278 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113278/1 /scratch/stefan/7770410/working/building/REAL300020113278 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 153) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/153 `/scratch/stefan/7770410/working/3D/153' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1) `REAL300020113278.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113278 none CC1=NC=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 39, 57, 62, 62, 62, 62, 13, 13, 1, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 13, 39, 39, 57, 57, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40]) total number of confs: 262 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113278 none CC1=NC=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 91, 91, 91, 48, 48, 48, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 91, 91, 91, 91, 91, 48, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [36, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 237 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113278 none CC1=NC=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 91, 91, 91, 169, 201, 201, 201, 201, 201, 91, 91, 11, 1, 2, 2, 2, 1, 3, 11, 11, 11, 11, 91, 169, 169, 201, 201, 11, 11] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 26, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 729 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113278 none CC1=NC=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 141, 141, 141, 61, 61, 61, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 61, 201, 201, 201, 201, 201, 141, 61, 61, 61, 61, 10, 6, 6, 4, 4, 61, 61] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 515 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113278 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113278 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113278/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113278/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113278 Building REAL300020113279 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113279' /scratch/stefan/7770410/working/building/REAL300020113279 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113279 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113279/0 /scratch/stefan/7770410/working/building/REAL300020113279 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/154 `/scratch/stefan/7770410/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1) `REAL300020113279.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113279 none COC1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 9, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 54, 76, 92, 92, 92, 92, 13, 13, 1, 9, 9, 9, 9, 9, 9, 6, 1, 1, 1, 1, 13, 54, 54, 76, 76, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 355 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113279 none COC1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 76, 76, 76, 57, 57, 57, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 13, 76, 76, 76, 76, 76, 76, 57, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13] 201 rigid atoms, others: [37, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 222 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113279 none COC1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 76, 76, 76, 166, 201, 201, 201, 201, 201, 76, 76, 9, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 9, 76, 166, 166, 201, 201, 9, 9] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 26, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 749 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113279 none COC1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 88, 88, 88, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 88, 201, 201, 201, 201, 201, 201, 201, 88, 88, 88, 88, 15, 6, 6, 4, 4, 88, 88] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 554 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113279 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113279/1 /scratch/stefan/7770410/working/building/REAL300020113279 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 155) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/155 `/scratch/stefan/7770410/working/3D/155' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1) `REAL300020113279.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113279/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113279 none COC1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 9, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 53, 75, 87, 87, 87, 87, 13, 13, 1, 9, 9, 9, 9, 9, 9, 6, 1, 1, 1, 1, 13, 53, 53, 75, 75, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 344 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113279 none COC1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 76, 76, 76, 57, 57, 57, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 13, 76, 76, 76, 76, 76, 76, 57, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13] 201 rigid atoms, others: [37, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 222 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113279 none COC1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 76, 76, 76, 166, 201, 201, 201, 201, 201, 76, 76, 9, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 9, 76, 166, 166, 201, 201, 9, 9] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 26, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 743 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113279 none COC1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 88, 88, 88, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 88, 201, 201, 201, 201, 201, 201, 201, 88, 88, 88, 88, 14, 6, 6, 4, 4, 88, 88] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 557 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113279 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113279 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113279/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113279/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113279 Building REAL300020113280 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113280' /scratch/stefan/7770410/working/building/REAL300020113280 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113280 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113280/0 /scratch/stefan/7770410/working/building/REAL300020113280 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/156 `/scratch/stefan/7770410/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H](CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(N)=O) `REAL300020113280.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113280 none CC(=O)N[C@@H](CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 11, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [137, 137, 137, 99, 88, 99, 35, 35, 35, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 9, 99, 129, 129, 137, 137, 137, 137, 88, 88, 35, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 129, 129] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 675 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113280 none CC(=O)N[C@@H](CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 11, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 199, 199, 172, 165, 172, 95, 95, 95, 35, 35, 35, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 35, 172, 196, 196, 199, 199, 199, 199, 165, 165, 95, 35, 35, 35, 35, 7, 4, 4, 2, 2, 35, 35, 196, 196] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 854 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113280 none CC(=O)N[C@@H](CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 11, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 25, 20, 25, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 29, 41, 42, 42, 42, 42, 9, 9, 1, 25, 47, 47, 49, 49, 49, 49, 20, 20, 6, 1, 1, 1, 1, 9, 29, 29, 41, 41, 1, 1, 47, 47] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 417 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113280 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113280/1 /scratch/stefan/7770410/working/building/REAL300020113280 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 157) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/157 `/scratch/stefan/7770410/working/3D/157' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H](CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(N)=O) `REAL300020113280.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113280 none CC(=O)N[C@@H](CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 11, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [136, 136, 136, 100, 89, 100, 35, 35, 35, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 9, 100, 128, 128, 136, 136, 136, 136, 89, 89, 35, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 128, 128] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 666 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113280 none CC(=O)N[C@@H](CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 11, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 199, 199, 173, 165, 173, 95, 95, 95, 35, 35, 35, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 35, 173, 197, 197, 199, 199, 199, 199, 165, 165, 95, 35, 35, 35, 35, 7, 4, 4, 2, 2, 35, 35, 197, 197] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 856 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113280 none CC(=O)N[C@@H](CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 11, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 26, 21, 26, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 29, 41, 42, 42, 42, 42, 9, 9, 1, 26, 49, 49, 49, 49, 49, 49, 21, 21, 6, 1, 1, 1, 1, 9, 29, 29, 41, 41, 1, 1, 49, 49] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 420 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113280 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113280 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113280/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113280/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113280 Building REAL300020113281 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113281' /scratch/stefan/7770410/working/building/REAL300020113281 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113281 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113281/0 /scratch/stefan/7770410/working/building/REAL300020113281 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/158 `/scratch/stefan/7770410/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CS1) `REAL300020113281.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113281 none CC1=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 24, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 22, 34, 37, 37, 37, 37, 8, 8, 1, 41, 41, 41, 41, 41, 41, 24, 24, 5, 1, 1, 1, 1, 8, 22, 22, 34, 34, 1, 1, 41, 41] 201 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44]) total number of confs: 258 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113281 none CC1=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [129, 129, 95, 19, 19, 19, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 8, 129, 129, 129, 129, 129, 129, 95, 95, 19, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8, 129, 129] 201 rigid atoms, others: [36, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 415 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113281 none CC1=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 21, 21, 21, 41, 41, 41, 129, 129, 129, 181, 201, 201, 201, 201, 201, 129, 129, 41, 1, 1, 1, 2, 2, 2, 6, 6, 21, 41, 41, 41, 41, 129, 181, 181, 201, 201, 41, 41, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 43, 44, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 639 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113281 none CC1=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 168, 57, 57, 57, 37, 37, 37, 9, 9, 9, 6, 4, 1, 1, 1, 1, 1, 1, 9, 9, 37, 201, 201, 201, 201, 201, 201, 168, 168, 57, 37, 37, 37, 37, 9, 6, 6, 4, 4, 37, 37, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 682 number of broken/clashed sets: 3 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113281 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113281/1 /scratch/stefan/7770410/working/building/REAL300020113281 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 159) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/159 `/scratch/stefan/7770410/working/3D/159' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CS1) `REAL300020113281.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113281/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113281 none CC1=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 24, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 22, 34, 37, 37, 37, 37, 8, 8, 1, 41, 41, 41, 41, 41, 41, 24, 24, 5, 1, 1, 1, 1, 8, 22, 22, 34, 34, 1, 1, 41, 41] 201 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44]) total number of confs: 258 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113281 none CC1=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [130, 130, 96, 19, 19, 19, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 8, 130, 130, 130, 130, 130, 130, 96, 96, 19, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8, 130, 130] 201 rigid atoms, others: [36, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 418 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113281 none CC1=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 21, 21, 21, 41, 41, 41, 130, 130, 130, 181, 201, 201, 201, 201, 201, 130, 130, 41, 1, 1, 1, 2, 2, 2, 6, 6, 21, 41, 41, 41, 41, 130, 181, 181, 201, 201, 41, 41, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 43, 44, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 634 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113281 none CC1=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 168, 57, 57, 57, 37, 37, 37, 9, 9, 9, 6, 4, 1, 1, 1, 1, 1, 1, 9, 9, 37, 201, 201, 201, 201, 201, 201, 168, 168, 57, 37, 37, 37, 37, 9, 6, 6, 4, 4, 37, 37, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 679 number of broken/clashed sets: 3 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113281 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113281 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113281/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113281/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113281 Building REAL300020113282 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113282' /scratch/stefan/7770410/working/building/REAL300020113282 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113282 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113282/0 /scratch/stefan/7770410/working/building/REAL300020113282 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/160 `/scratch/stefan/7770410/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CSC(C2CC2)=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113282.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113282 none O=C(CC1=CSC(C2CC2)=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 5, 5, 5, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 13, 7, 7, 7, 7, 1, 1, 1, 1, 7, 26, 26, 46, 46, 46, 114, 114, 114, 173, 201, 201, 201, 201, 201, 114, 114, 46, 13, 13, 7, 1, 1, 1, 1, 1, 26, 46, 46, 46, 46, 114, 173, 173, 201, 201, 46, 46] 201 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 31] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 742 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113282 none O=C(CC1=CSC(C2CC2)=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 5, 5, 5, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 124, 124, 124, 124, 124, 201, 201, 124, 31, 31, 31, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 31, 124, 124, 124, 201, 201, 201, 201, 201, 47, 31, 31, 31, 31, 8, 4, 4, 2, 2, 31, 31] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 785 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113282 none O=C(CC1=CSC(C2CC2)=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 5, 5, 5, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 15, 15, 15, 15, 15, 46, 46, 15, 1, 1, 1, 1, 1, 7, 7, 7, 18, 30, 30, 30, 30, 30, 7, 7, 1, 15, 15, 15, 46, 46, 46, 46, 46, 5, 1, 1, 1, 1, 7, 18, 18, 30, 30, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 263 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113282 none O=C(CC1=CSC(C2CC2)=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 5, 5, 5, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 1, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 15, 15, 15, 53, 53, 53, 95, 122, 122, 122, 122, 122, 53, 53, 15, 3, 3, 1, 7, 7, 7, 7, 7, 7, 15, 15, 15, 15, 53, 95, 95, 122, 122, 15, 15] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 10, 30] set([0, 1, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 491 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113282 none O=C(CC1=CSC(C2CC2)=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 5, 5, 5, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 53, 53, 53, 53, 53, 114, 114, 53, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 53, 53, 53, 114, 114, 114, 114, 114, 15, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 422 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113282 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113282/1 /scratch/stefan/7770410/working/building/REAL300020113282 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 161) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/161 `/scratch/stefan/7770410/working/3D/161' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CSC(C2CC2)=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113282.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113282 none O=C(CC1=CSC(C2CC2)=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 5, 5, 5, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 13, 7, 7, 7, 7, 1, 1, 1, 1, 7, 26, 26, 46, 46, 46, 116, 116, 116, 173, 201, 201, 201, 201, 201, 116, 116, 46, 13, 13, 7, 1, 1, 1, 1, 1, 26, 46, 46, 46, 46, 116, 173, 173, 201, 201, 46, 46] 201 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 31] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 736 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113282 none O=C(CC1=CSC(C2CC2)=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 5, 5, 5, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 123, 123, 123, 123, 123, 201, 201, 123, 31, 31, 31, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 31, 123, 123, 123, 201, 201, 201, 201, 201, 47, 31, 31, 31, 31, 8, 4, 4, 2, 2, 31, 31] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 785 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113282 none O=C(CC1=CSC(C2CC2)=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 5, 5, 5, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 15, 15, 15, 15, 15, 46, 46, 15, 1, 1, 1, 1, 1, 7, 7, 7, 18, 30, 30, 30, 30, 30, 7, 7, 1, 15, 15, 15, 46, 46, 46, 46, 46, 5, 1, 1, 1, 1, 7, 18, 18, 30, 30, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 265 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113282 none O=C(CC1=CSC(C2CC2)=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 5, 5, 5, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 1, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 15, 15, 15, 54, 54, 54, 95, 122, 122, 122, 122, 122, 54, 54, 15, 3, 3, 1, 7, 7, 7, 7, 7, 7, 15, 15, 15, 15, 54, 95, 95, 122, 122, 15, 15] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 10, 30] set([0, 1, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 490 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113282 none O=C(CC1=CSC(C2CC2)=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 5, 5, 5, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 54, 54, 54, 54, 54, 116, 116, 54, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 54, 54, 54, 116, 116, 116, 116, 116, 16, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 428 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113282 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113282 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113282/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113282/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113282 Building REAL300020113283 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113283' /scratch/stefan/7770410/working/building/REAL300020113283 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113283 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113283/0 /scratch/stefan/7770410/working/building/REAL300020113283 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/162 `/scratch/stefan/7770410/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1C) `REAL300020113283.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113283 none CC(C)C1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 69, 91, 112, 112, 112, 112, 13, 13, 1, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 13, 69, 69, 91, 91, 1, 1, 13, 13, 13] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 46, 47, 40, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50]) total number of confs: 414 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113283 none CC(C)C1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 81, 81, 51, 51, 51, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 20, 20, 20, 20, 1, 1, 13, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 51, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 81, 81, 81] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 247 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113283 none CC(C)C1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 3, 3, 4, 13, 13, 13, 81, 81, 81, 159, 201, 201, 201, 201, 201, 81, 81, 13, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 1, 4, 13, 13, 13, 13, 81, 159, 159, 201, 201, 13, 13, 2, 2, 2] 201 rigid atoms, others: [1, 3, 4, 5, 6, 35, 25, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 749 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113283 none CC(C)C1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 200, 200, 200, 113, 113, 113, 22, 22, 22, 6, 4, 1, 1, 1, 1, 1, 1, 22, 22, 113, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 200, 113, 113, 113, 113, 22, 6, 6, 4, 4, 113, 113, 201, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 548 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113283 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113283/1 /scratch/stefan/7770410/working/building/REAL300020113283 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 163) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/163 `/scratch/stefan/7770410/working/3D/163' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1C) `REAL300020113283.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113283 none CC(C)C1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 69, 91, 112, 112, 112, 112, 13, 13, 1, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 13, 69, 69, 91, 91, 1, 1, 13, 13, 13] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 46, 47, 40, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50]) total number of confs: 414 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113283 none CC(C)C1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 81, 81, 51, 51, 51, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 20, 20, 20, 20, 1, 1, 13, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 51, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 81, 81, 81] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 247 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113283 none CC(C)C1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 3, 3, 4, 13, 13, 13, 81, 81, 81, 159, 201, 201, 201, 201, 201, 81, 81, 13, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 1, 4, 13, 13, 13, 13, 81, 159, 159, 201, 201, 13, 13, 2, 2, 2] 201 rigid atoms, others: [1, 3, 4, 5, 6, 35, 25, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 749 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113283 none CC(C)C1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 200, 200, 200, 113, 113, 113, 22, 22, 22, 6, 4, 1, 1, 1, 1, 1, 1, 22, 22, 113, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 200, 113, 113, 113, 113, 22, 6, 6, 4, 4, 113, 113, 201, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 548 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113283 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113283 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113283/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113283/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113283 Building REAL300020113284 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113284' /scratch/stefan/7770410/working/building/REAL300020113284 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113284 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113284/0 /scratch/stefan/7770410/working/building/REAL300020113284 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/164 `/scratch/stefan/7770410/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(C)C) `REAL300020113284.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113284 none CCOC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 67, 39, 39, 39, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 11, 11, 11, 11, 1, 1, 11, 67, 104, 104, 76, 76, 76, 76, 76, 67, 39, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 104, 104, 104, 104, 104, 104, 104] 201 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 502 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113284 none CCOC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [195, 195, 183, 99, 99, 99, 41, 41, 41, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 41, 183, 201, 201, 195, 195, 195, 195, 195, 183, 99, 41, 41, 41, 41, 9, 4, 4, 2, 2, 41, 41, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 815 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113284 none CCOC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 14, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 32, 46, 55, 55, 55, 55, 11, 11, 1, 14, 28, 28, 18, 18, 18, 18, 18, 14, 6, 1, 1, 1, 1, 11, 32, 32, 46, 46, 1, 1, 28, 28, 28, 28, 28, 28, 28] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 326 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113284 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113284/1 /scratch/stefan/7770410/working/building/REAL300020113284 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 165) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/165 `/scratch/stefan/7770410/working/3D/165' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(C)C) `REAL300020113284.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113284 none CCOC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 67, 39, 39, 39, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 11, 11, 11, 11, 1, 1, 11, 67, 104, 104, 76, 76, 76, 76, 76, 67, 39, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 104, 104, 104, 104, 104, 104, 104] 201 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 496 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113284 none CCOC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [195, 195, 183, 100, 100, 100, 42, 42, 42, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 42, 183, 201, 201, 195, 195, 195, 195, 195, 183, 100, 42, 42, 42, 42, 9, 4, 4, 2, 2, 42, 42, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 809 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113284 none CCOC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 15, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 32, 46, 55, 55, 55, 55, 11, 11, 1, 15, 28, 28, 20, 20, 20, 20, 20, 15, 6, 1, 1, 1, 1, 11, 32, 32, 46, 46, 1, 1, 28, 28, 28, 28, 28, 28, 28] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 325 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113284 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113284 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113284/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113284/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113284 Building REAL300020113285 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113285' /scratch/stefan/7770410/working/building/REAL300020113285 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113285 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113285/0 /scratch/stefan/7770410/working/building/REAL300020113285 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/166 `/scratch/stefan/7770410/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(C)OCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113285.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113285 none CC(C)CC(C)OCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 102, 101, 102, 75, 72, 23, 23, 23, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 107, 107, 107, 107, 107, 107, 107, 107, 107, 102, 102, 102, 102, 75, 75, 72, 72, 23, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [18, 14, 15, 16, 17, 50, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56]) total number of confs: 382 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113285 none CC(C)CC(C)OCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 194, 193, 82, 82, 82, 38, 38, 38, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 38, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 194, 194, 193, 193, 82, 38, 38, 38, 38, 8, 4, 4, 2, 2, 38, 38] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 711 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113285 none CC(C)CC(C)OCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 40, 39, 40, 26, 24, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 26, 38, 38, 38, 38, 38, 8, 8, 1, 46, 46, 46, 46, 46, 46, 46, 46, 46, 40, 40, 40, 40, 26, 26, 24, 24, 6, 1, 1, 1, 1, 8, 26, 26, 38, 38, 1, 1] 201 rigid atoms, others: [15, 11, 12, 13, 14, 47, 48, 49, 46, 55, 56, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53, 54]) total number of confs: 311 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113285 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113285/1 /scratch/stefan/7770410/working/building/REAL300020113285 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 167) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/167 `/scratch/stefan/7770410/working/3D/167' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(C)OCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113285.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113285/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113285 none CC(C)CC(C)OCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 102, 101, 102, 75, 72, 23, 23, 23, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 107, 107, 107, 107, 107, 107, 107, 107, 107, 102, 102, 102, 102, 75, 75, 72, 72, 23, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [18, 14, 15, 16, 17, 50, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56]) total number of confs: 382 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113285 none CC(C)CC(C)OCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 194, 193, 82, 82, 82, 38, 38, 38, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 38, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 194, 194, 193, 193, 82, 38, 38, 38, 38, 8, 4, 4, 2, 2, 38, 38] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 711 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113285 none CC(C)CC(C)OCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 40, 39, 40, 26, 24, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 26, 38, 38, 38, 38, 38, 8, 8, 1, 46, 46, 46, 46, 46, 46, 46, 46, 46, 40, 40, 40, 40, 26, 26, 24, 24, 6, 1, 1, 1, 1, 8, 26, 26, 38, 38, 1, 1] 201 rigid atoms, others: [15, 11, 12, 13, 14, 47, 48, 49, 46, 55, 56, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53, 54]) total number of confs: 311 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113285 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113285 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113285/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113285/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113285 Building REAL300020113286 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113286' /scratch/stefan/7770410/working/building/REAL300020113286 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113286 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113286/0 /scratch/stefan/7770410/working/building/REAL300020113286 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/168 `/scratch/stefan/7770410/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)N1CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113286.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113286 none O=C(CNC(=O)N1CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 8, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 32, 38, 38, 38, 48, 48, 48, 43, 1, 1, 1, 1, 1, 8, 8, 8, 30, 43, 43, 43, 43, 43, 8, 8, 1, 32, 32, 38, 48, 48, 48, 48, 48, 48, 48, 48, 5, 1, 1, 1, 1, 8, 30, 30, 43, 43, 1, 1] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 346 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113286 none O=C(CNC(=O)N1CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 8, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 100, 102, 102, 102, 113, 113, 113, 101, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 100, 100, 102, 113, 113, 113, 113, 113, 113, 113, 113, 24, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 465 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113286 none O=C(CNC(=O)N1CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 8, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 23, 23, 48, 48, 48, 113, 113, 113, 175, 201, 201, 201, 201, 201, 113, 113, 48, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 25, 48, 48, 48, 48, 113, 175, 175, 201, 201, 48, 48] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 36, 38, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 721 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113286 none O=C(CNC(=O)N1CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 8, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 201, 201, 201, 201, 201, 201, 201, 187, 43, 43, 43, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 43, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 80, 43, 43, 43, 43, 8, 4, 4, 2, 2, 43, 43] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 768 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113286 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113286/1 /scratch/stefan/7770410/working/building/REAL300020113286 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 169) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/169 `/scratch/stefan/7770410/working/3D/169' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)N1CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113286.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113286 none O=C(CNC(=O)N1CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 8, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 32, 38, 38, 38, 47, 47, 47, 42, 1, 1, 1, 1, 1, 8, 8, 8, 30, 43, 43, 43, 43, 43, 8, 8, 1, 32, 32, 38, 47, 47, 47, 47, 47, 47, 47, 47, 5, 1, 1, 1, 1, 8, 30, 30, 43, 43, 1, 1] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 344 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113286 none O=C(CNC(=O)N1CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 8, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 100, 103, 103, 103, 113, 113, 113, 101, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 100, 100, 103, 113, 113, 113, 113, 113, 113, 113, 113, 24, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 467 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113286 none O=C(CNC(=O)N1CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 8, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 23, 23, 47, 47, 47, 113, 113, 113, 175, 201, 201, 201, 201, 201, 113, 113, 47, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 25, 47, 47, 47, 47, 113, 175, 175, 201, 201, 47, 47] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 36, 38, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 719 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113286 none O=C(CNC(=O)N1CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 8, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 201, 201, 201, 201, 201, 201, 201, 187, 43, 43, 43, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 43, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 80, 43, 43, 43, 43, 8, 4, 4, 2, 2, 43, 43] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 768 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113286 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113286 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113286/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113286/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113286 Building REAL300020113287 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113287' /scratch/stefan/7770410/working/building/REAL300020113287 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113287 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113287/0 /scratch/stefan/7770410/working/building/REAL300020113287 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/170 `/scratch/stefan/7770410/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=N1) `REAL300020113287.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113287 none COCCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 74, 54, 16, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 33, 40, 50, 50, 50, 50, 7, 7, 1, 16, 16, 95, 95, 95, 74, 74, 54, 54, 16, 5, 1, 1, 1, 1, 7, 33, 33, 40, 40, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 507 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113287 none COCCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 107, 85, 33, 33, 33, 14, 14, 14, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 7, 33, 33, 124, 124, 124, 107, 107, 85, 85, 33, 14, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 505 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113287 none COCCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 10, 6, 1, 1, 1, 1, 1, 7, 7, 7, 16, 16, 16, 33, 33, 33, 90, 102, 114, 114, 114, 114, 33, 33, 16, 1, 1, 25, 25, 25, 10, 10, 6, 6, 1, 7, 16, 16, 16, 16, 33, 90, 90, 102, 102, 16, 16] 201 rigid atoms, others: [35, 4, 5, 6, 7, 3, 26, 27] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 468 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113287 none COCCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 187, 125, 125, 125, 85, 85, 85, 61, 61, 61, 25, 25, 25, 7, 4, 1, 1, 1, 1, 1, 1, 25, 25, 61, 125, 125, 201, 201, 201, 201, 201, 187, 187, 125, 85, 61, 61, 61, 61, 25, 7, 7, 4, 4, 61, 61] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 739 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113287 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113287/1 /scratch/stefan/7770410/working/building/REAL300020113287 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 171) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/171 `/scratch/stefan/7770410/working/3D/171' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=N1) `REAL300020113287.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113287 none COCCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 74, 54, 16, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 33, 40, 50, 50, 50, 50, 7, 7, 1, 16, 16, 96, 96, 96, 74, 74, 54, 54, 16, 5, 1, 1, 1, 1, 7, 33, 33, 40, 40, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 509 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113287 none COCCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 106, 84, 33, 33, 33, 14, 14, 14, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 7, 33, 33, 124, 124, 124, 106, 106, 84, 84, 33, 14, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 504 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113287 none COCCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 10, 6, 1, 1, 1, 1, 1, 7, 7, 7, 16, 16, 16, 33, 33, 33, 91, 103, 115, 115, 115, 115, 33, 33, 16, 1, 1, 26, 26, 26, 10, 10, 6, 6, 1, 7, 16, 16, 16, 16, 33, 91, 91, 103, 103, 16, 16] 201 rigid atoms, others: [35, 4, 5, 6, 7, 3, 26, 27] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 469 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113287 none COCCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 188, 125, 125, 125, 85, 85, 85, 62, 62, 62, 25, 25, 25, 7, 4, 1, 1, 1, 1, 1, 1, 25, 25, 62, 125, 125, 201, 201, 201, 201, 201, 188, 188, 125, 85, 62, 62, 62, 62, 25, 7, 7, 4, 4, 62, 62] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 731 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113287 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113287 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113287/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113287/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113287 Building REAL300020113288 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113288' /scratch/stefan/7770410/working/building/REAL300020113288 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113288 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113288/0 /scratch/stefan/7770410/working/building/REAL300020113288 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/172 `/scratch/stefan/7770410/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C(C)(C)C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113288.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113288 none CC1=NN(C(C)(C)C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 33, 33, 33, 16, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 27, 35, 42, 42, 42, 42, 6, 6, 1, 16, 16, 16, 33, 33, 33, 33, 33, 33, 33, 33, 33, 16, 6, 1, 1, 1, 1, 6, 27, 27, 35, 35, 1, 1] 101 rigid atoms, others: [45, 44, 43, 12, 13, 14, 15, 16, 52, 46, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 255 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113288 none CC1=NN(C(C)(C)C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 39, 60, 60, 60, 39, 21, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 6, 39, 39, 39, 60, 60, 60, 60, 60, 60, 60, 60, 60, 39, 21, 6, 6, 6, 6, 1, 8, 8, 10, 10, 6, 6] 101 rigid atoms, others: [15, 47, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 232 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113288 none CC1=NN(C(C)(C)C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 5, 5, 5, 16, 16, 16, 39, 39, 39, 82, 95, 101, 101, 101, 101, 39, 39, 16, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 5, 16, 16, 16, 16, 39, 82, 82, 95, 95, 16, 16] 101 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 41] set([5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 369 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113288 none CC1=NN(C(C)(C)C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 101, 101, 101, 101, 101, 101, 84, 84, 84, 45, 45, 45, 17, 17, 17, 7, 4, 1, 1, 1, 1, 1, 1, 17, 17, 45, 101, 101, 101, 101, 101, 101, 101, 101, 101, 101, 101, 101, 101, 84, 45, 45, 45, 45, 17, 7, 7, 4, 4, 45, 45] 101 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 275 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113288 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113288/1 /scratch/stefan/7770410/working/building/REAL300020113288 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 173) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/173 `/scratch/stefan/7770410/working/3D/173' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C(C)(C)C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113288.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113288 none CC1=NN(C(C)(C)C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 33, 33, 33, 16, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 27, 35, 42, 42, 42, 42, 6, 6, 1, 16, 16, 16, 33, 33, 33, 33, 33, 33, 33, 33, 33, 16, 6, 1, 1, 1, 1, 6, 27, 27, 35, 35, 1, 1] 100 rigid atoms, others: [45, 44, 43, 12, 13, 14, 15, 16, 52, 46, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 255 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113288 none CC1=NN(C(C)(C)C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 39, 60, 60, 60, 39, 21, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 6, 39, 39, 39, 60, 60, 60, 60, 60, 60, 60, 60, 60, 39, 21, 6, 6, 6, 6, 1, 8, 8, 10, 10, 6, 6] 100 rigid atoms, others: [15, 47, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 232 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113288 none CC1=NN(C(C)(C)C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 5, 5, 5, 16, 16, 16, 39, 39, 39, 81, 94, 100, 100, 100, 100, 39, 39, 16, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 5, 16, 16, 16, 16, 39, 81, 81, 94, 94, 16, 16] 100 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 41] set([5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 366 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113288 none CC1=NN(C(C)(C)C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 100, 100, 100, 100, 100, 100, 84, 84, 84, 45, 45, 45, 16, 16, 16, 7, 4, 1, 1, 1, 1, 1, 1, 16, 16, 45, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 84, 45, 45, 45, 45, 16, 7, 7, 4, 4, 45, 45] 100 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 273 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113288 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113288 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113288/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113288/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113288 Building REAL300020113289 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113289' /scratch/stefan/7770410/working/building/REAL300020113289 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113289 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113289/0 /scratch/stefan/7770410/working/building/REAL300020113289 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/174 `/scratch/stefan/7770410/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[N@@H+]1CCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113289.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113289 none CC(C)[N@@H+]1CCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [15, 12, 15, 12, 12, 12, 12, 12, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 13, 13, 13, 13, 13, 13, 12, 12, 1, 15, 15, 15, 15, 15, 15, 15, 12, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 12, 13, 13, 13, 13, 1, 1] 41 rigid atoms, others: [11, 15, 44, 43, 12, 13, 14, 45, 52, 46, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 66 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113289 none CC(C)[N@@H+]1CCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 40, 30, 30, 30, 12, 12, 12, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 12, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 30, 12, 12, 12, 12, 1, 4, 4, 4, 4, 12, 12] 41 rigid atoms, others: [14, 47, 16, 17, 18, 25, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 125 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113289 none CC(C)[N@@H+]1CCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 40, 40, 40, 41, 41, 41, 41, 41, 41, 40, 40, 12, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 40, 41, 41, 41, 41, 12, 12] 41 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 39, 40, 35, 41, 36, 38, 37] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 82 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113289 none CC(C)[N@@H+]1CCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 41, 31, 31, 31, 13, 13, 13, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 31, 13, 13, 13, 13, 4, 3, 3, 1, 1, 13, 13] 41 rigid atoms, others: [19, 50, 18, 51, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 122 number of broken/clashed sets: 3 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113289 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113289/1 /scratch/stefan/7770410/working/building/REAL300020113289 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 175) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/175 `/scratch/stefan/7770410/working/3D/175' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[N@H+]1CCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113289.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113289/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113289 none CC(C)[N@H+]1CCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [16, 15, 16, 15, 15, 15, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 10, 10, 10, 10, 10, 10, 9, 9, 1, 16, 16, 16, 16, 16, 16, 16, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 9, 10, 10, 10, 10, 1, 1] 57 rigid atoms, others: [11, 15, 44, 43, 12, 13, 14, 45, 52, 46, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 62 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113289 none CC(C)[N@H+]1CCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 56, 56, 56, 56, 56, 34, 34, 34, 9, 9, 9, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 9, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 34, 9, 9, 9, 9, 1, 4, 4, 4, 4, 9, 9] 57 rigid atoms, others: [14, 47, 16, 17, 18, 25, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 179 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113289 none CC(C)[N@H+]1CCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 56, 56, 56, 57, 57, 57, 57, 57, 57, 56, 56, 15, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 15, 56, 57, 57, 57, 57, 15, 15] 57 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 39, 40, 35, 41, 36, 38, 37] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 104 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113289 none CC(C)[N@H+]1CCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 57, 57, 57, 57, 57, 37, 37, 37, 12, 12, 12, 6, 6, 6, 5, 2, 1, 1, 1, 1, 1, 1, 6, 6, 12, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 37, 12, 12, 12, 12, 6, 5, 5, 2, 2, 12, 12] 57 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 180 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113289 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113289 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113289/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113289/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113289 Building REAL300020113290 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113290' /scratch/stefan/7770410/working/building/REAL300020113290 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113290 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113290/0 /scratch/stefan/7770410/working/building/REAL300020113290 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/176 `/scratch/stefan/7770410/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCOCC1CC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113290.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113290 none O=C(CCOCC1CC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 18, 18, 21, 44, 63, 63, 1, 1, 1, 1, 1, 7, 7, 7, 19, 30, 30, 30, 30, 30, 7, 7, 1, 18, 18, 18, 18, 44, 44, 63, 63, 63, 63, 63, 5, 1, 1, 1, 1, 7, 19, 19, 30, 30, 1, 1] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 371 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113290 none O=C(CCOCC1CC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 51, 51, 58, 95, 128, 128, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 51, 51, 51, 51, 95, 95, 128, 128, 128, 128, 128, 16, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 557 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113290 none O=C(CCOCC1CC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 36, 22, 13, 5, 1, 1, 1, 1, 44, 44, 63, 63, 63, 128, 128, 128, 172, 201, 201, 201, 201, 201, 128, 128, 63, 36, 36, 22, 22, 5, 5, 1, 1, 1, 1, 1, 44, 63, 63, 63, 63, 128, 172, 172, 201, 201, 63, 63] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 751 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113290 none O=C(CCOCC1CC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 105, 105, 118, 171, 201, 201, 31, 31, 31, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 31, 105, 105, 105, 105, 171, 171, 201, 201, 201, 201, 201, 45, 31, 31, 31, 31, 7, 4, 4, 2, 2, 31, 31] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 800 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113290 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113290/1 /scratch/stefan/7770410/working/building/REAL300020113290 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 177) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/177 `/scratch/stefan/7770410/working/3D/177' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCOCC1CC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113290.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113290 none O=C(CCOCC1CC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 18, 18, 21, 44, 63, 63, 1, 1, 1, 1, 1, 7, 7, 7, 19, 30, 30, 30, 30, 30, 7, 7, 1, 18, 18, 18, 18, 44, 44, 63, 63, 63, 63, 63, 5, 1, 1, 1, 1, 7, 19, 19, 30, 30, 1, 1] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 371 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113290 none O=C(CCOCC1CC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 53, 53, 60, 96, 128, 128, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 53, 53, 53, 53, 96, 96, 128, 128, 128, 128, 128, 16, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 556 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113290 none O=C(CCOCC1CC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 36, 22, 13, 5, 1, 1, 1, 1, 44, 44, 63, 63, 63, 128, 128, 128, 172, 201, 201, 201, 201, 201, 128, 128, 63, 36, 36, 22, 22, 5, 5, 1, 1, 1, 1, 1, 44, 63, 63, 63, 63, 128, 172, 172, 201, 201, 63, 63] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 754 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113290 none O=C(CCOCC1CC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 106, 106, 119, 173, 201, 201, 32, 32, 32, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 32, 106, 106, 106, 106, 173, 173, 201, 201, 201, 201, 201, 45, 32, 32, 32, 32, 8, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 798 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113290 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113290 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113290/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113290/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113290 Building REAL300020113291 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113291' /scratch/stefan/7770410/working/building/REAL300020113291 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113291 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113291/0 /scratch/stefan/7770410/working/building/REAL300020113291 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/178 `/scratch/stefan/7770410/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113291.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113291 none CNS(=O)(=O)CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 92, 82, 92, 92, 76, 23, 23, 23, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 114, 114, 114, 114, 82, 82, 76, 76, 23, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 484 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113291 none CNS(=O)(=O)CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 192, 201, 201, 189, 85, 85, 85, 44, 44, 44, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 44, 201, 201, 201, 201, 192, 192, 189, 189, 85, 44, 44, 44, 44, 11, 6, 6, 4, 4, 44, 44] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 761 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113291 none CNS(=O)(=O)CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 37, 27, 37, 37, 23, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 25, 37, 38, 38, 38, 38, 8, 8, 1, 51, 51, 51, 51, 27, 27, 23, 23, 5, 1, 1, 1, 1, 8, 25, 25, 37, 37, 1, 1] 201 rigid atoms, others: [45, 35, 36, 37, 38, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 363 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113291 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113291/1 /scratch/stefan/7770410/working/building/REAL300020113291 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 179) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/179 `/scratch/stefan/7770410/working/3D/179' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113291.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113291/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113291 none CNS(=O)(=O)CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 92, 82, 92, 92, 77, 24, 24, 24, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 9, 114, 114, 114, 114, 82, 82, 77, 77, 24, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 480 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113291 none CNS(=O)(=O)CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 191, 201, 201, 188, 87, 87, 87, 45, 45, 45, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 45, 201, 201, 201, 201, 191, 191, 188, 188, 87, 45, 45, 45, 45, 11, 6, 6, 4, 4, 45, 45] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 758 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113291 none CNS(=O)(=O)CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 36, 26, 36, 36, 23, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 26, 38, 39, 39, 39, 39, 9, 9, 1, 50, 50, 50, 50, 26, 26, 23, 23, 5, 1, 1, 1, 1, 9, 26, 26, 38, 38, 1, 1] 201 rigid atoms, others: [45, 35, 36, 37, 38, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 358 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113291 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113291 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113291/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113291/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113291 Building REAL300020113292 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113292' /scratch/stefan/7770410/working/building/REAL300020113292 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113292 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113292/0 /scratch/stefan/7770410/working/building/REAL300020113292 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/180 `/scratch/stefan/7770410/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1) `REAL300020113292.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113292 none CC1CC1C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 51, 51, 51, 103, 137, 137, 137, 137, 137, 51, 51, 7, 1, 6, 6, 6, 6, 6, 6, 6, 1, 1, 3, 7, 7, 7, 7, 51, 103, 103, 137, 137, 7, 7] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 3, 36, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 528 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113292 none CC1CC1C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 137, 137, 137, 137, 136, 136, 136, 51, 51, 51, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 51, 137, 201, 201, 201, 201, 201, 201, 201, 137, 137, 136, 51, 51, 51, 51, 8, 4, 4, 2, 2, 51, 51] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 633 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113292 none CC1CC1C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 7, 7, 7, 7, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 34, 51, 51, 51, 51, 51, 13, 13, 1, 7, 20, 20, 20, 20, 20, 20, 20, 7, 7, 6, 1, 1, 1, 1, 13, 34, 34, 51, 51, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 259 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113292 none CC1CC1C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 6, 6, 7, 7, 7, 20, 20, 20, 110, 110, 110, 173, 201, 201, 201, 201, 201, 110, 110, 20, 6, 2, 2, 2, 1, 1, 1, 1, 6, 6, 7, 20, 20, 20, 20, 110, 173, 173, 201, 201, 20, 20] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 675 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113292 none CC1CC1C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 51, 51, 51, 51, 50, 50, 50, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 51, 110, 110, 110, 110, 110, 110, 110, 51, 51, 50, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 355 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113292 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113292/1 /scratch/stefan/7770410/working/building/REAL300020113292 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 181) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/181 `/scratch/stefan/7770410/working/3D/181' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1) `REAL300020113292.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113292 none CC1CC1C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 51, 51, 51, 103, 137, 137, 137, 137, 137, 51, 51, 7, 1, 6, 6, 6, 6, 6, 6, 6, 1, 1, 3, 7, 7, 7, 7, 51, 103, 103, 137, 137, 7, 7] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 3, 36, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 528 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113292 none CC1CC1C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 137, 137, 137, 137, 136, 136, 136, 51, 51, 51, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 51, 137, 201, 201, 201, 201, 201, 201, 201, 137, 137, 136, 51, 51, 51, 51, 8, 4, 4, 2, 2, 51, 51] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 633 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113292 none CC1CC1C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 7, 7, 7, 7, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 34, 51, 51, 51, 51, 51, 13, 13, 1, 7, 20, 20, 20, 20, 20, 20, 20, 7, 7, 6, 1, 1, 1, 1, 13, 34, 34, 51, 51, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 259 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113292 none CC1CC1C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 6, 6, 7, 7, 7, 20, 20, 20, 110, 110, 110, 173, 201, 201, 201, 201, 201, 110, 110, 20, 6, 2, 2, 2, 1, 1, 1, 1, 6, 6, 7, 20, 20, 20, 20, 110, 173, 173, 201, 201, 20, 20] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 675 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113292 none CC1CC1C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 51, 51, 51, 51, 50, 50, 50, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 51, 110, 110, 110, 110, 110, 110, 110, 51, 51, 50, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 355 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113292 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113292 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113292/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113292/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113292 Building REAL300020113293 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113293' /scratch/stefan/7770410/working/building/REAL300020113293 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113293 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113293/0 /scratch/stefan/7770410/working/building/REAL300020113293 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/182 `/scratch/stefan/7770410/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=NO1) `REAL300020113293.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113293 none CCCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 26, 26, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 20, 30, 30, 30, 30, 30, 8, 8, 1, 26, 26, 26, 26, 38, 38, 38, 38, 38, 38, 38, 5, 1, 1, 1, 1, 8, 20, 20, 30, 30, 1, 1, 26, 26, 26] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 45, 46, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 221 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113293 none CCCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 98, 98, 25, 25, 25, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 98, 98, 98, 98, 134, 134, 134, 134, 134, 134, 134, 25, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 98, 98, 98] 201 rigid atoms, others: [40, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 390 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113293 none CCCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 11, 11, 11, 26, 26, 26, 98, 98, 98, 125, 152, 152, 152, 152, 152, 98, 98, 26, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 11, 26, 26, 26, 26, 98, 125, 125, 152, 152, 26, 26, 2, 2, 2] 201 rigid atoms, others: [2, 3, 4, 5, 24, 25, 26, 27] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 496 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113293 none CCCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 157, 157, 59, 59, 59, 35, 35, 35, 10, 10, 10, 4, 2, 1, 1, 1, 1, 1, 1, 10, 10, 35, 157, 157, 157, 157, 201, 201, 201, 201, 201, 201, 201, 59, 35, 35, 35, 35, 10, 4, 4, 2, 2, 35, 35, 157, 157, 157] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 581 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113293 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113293/1 /scratch/stefan/7770410/working/building/REAL300020113293 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 183) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/183 `/scratch/stefan/7770410/working/3D/183' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=NO1) `REAL300020113293.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113293 none CCCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 26, 26, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 20, 30, 30, 30, 30, 30, 8, 8, 1, 26, 26, 26, 26, 38, 38, 38, 38, 38, 38, 38, 5, 1, 1, 1, 1, 8, 20, 20, 30, 30, 1, 1, 26, 26, 26] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 45, 46, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 221 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113293 none CCCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 98, 98, 25, 25, 25, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 98, 98, 98, 98, 134, 134, 134, 134, 134, 134, 134, 25, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 98, 98, 98] 201 rigid atoms, others: [40, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 390 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113293 none CCCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 11, 11, 11, 26, 26, 26, 98, 98, 98, 125, 152, 152, 152, 152, 152, 98, 98, 26, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 11, 26, 26, 26, 26, 98, 125, 125, 152, 152, 26, 26, 2, 2, 2] 201 rigid atoms, others: [2, 3, 4, 5, 24, 25, 26, 27] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 496 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113293 none CCCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 157, 157, 58, 58, 58, 34, 34, 34, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 34, 157, 157, 157, 157, 201, 201, 201, 201, 201, 201, 201, 58, 34, 34, 34, 34, 9, 4, 4, 2, 2, 34, 34, 157, 157, 157] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 580 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113293 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113293 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113293/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113293/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113293 Building REAL300020113294 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113294' /scratch/stefan/7770410/working/building/REAL300020113294 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113294 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113294/0 /scratch/stefan/7770410/working/building/REAL300020113294 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/184 `/scratch/stefan/7770410/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCOC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113294.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113294 none CCCCCCOC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 112, 60, 32, 30, 21, 30, 21, 21, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 60, 60, 30, 30, 30, 30, 21, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [18, 14, 15, 16, 17, 50, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56]) total number of confs: 545 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113294 none CCCCCCOC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 115, 68, 65, 53, 65, 53, 53, 34, 34, 34, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 34, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 115, 115, 65, 65, 65, 65, 53, 34, 34, 34, 34, 9, 4, 4, 2, 2, 34, 34] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 898 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113294 none CCCCCCOC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 18, 9, 7, 5, 7, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 20, 32, 32, 32, 32, 32, 7, 7, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 18, 18, 7, 7, 7, 7, 5, 1, 1, 1, 1, 7, 20, 20, 32, 32, 1, 1] 201 rigid atoms, others: [15, 11, 12, 13, 14, 47, 48, 49, 46, 55, 56, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53, 54]) total number of confs: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113294 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113294/1 /scratch/stefan/7770410/working/building/REAL300020113294 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 185) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/185 `/scratch/stefan/7770410/working/3D/185' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCOC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113294.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113294/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113294 none CCCCCCOC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 112, 60, 32, 30, 21, 30, 21, 21, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 60, 60, 30, 30, 30, 30, 21, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [18, 14, 15, 16, 17, 50, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56]) total number of confs: 545 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113294 none CCCCCCOC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 116, 66, 63, 52, 63, 52, 52, 33, 33, 33, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 33, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 116, 116, 63, 63, 63, 63, 52, 33, 33, 33, 33, 8, 4, 4, 2, 2, 33, 33] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 900 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113294 none CCCCCCOC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 18, 9, 7, 5, 7, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 20, 32, 32, 32, 32, 32, 7, 7, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 18, 18, 7, 7, 7, 7, 5, 1, 1, 1, 1, 7, 20, 20, 32, 32, 1, 1] 201 rigid atoms, others: [15, 11, 12, 13, 14, 47, 48, 49, 46, 55, 56, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53, 54]) total number of confs: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113294 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113294 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113294/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113294/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113294 Building REAL300020113295 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113295' /scratch/stefan/7770410/working/building/REAL300020113295 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113295 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113295/0 /scratch/stefan/7770410/working/building/REAL300020113295 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/186 `/scratch/stefan/7770410/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCOCCCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113295.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113295 none C=CCCOCCCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [137, 134, 69, 63, 55, 42, 42, 38, 10, 10, 10, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 6, 137, 137, 137, 134, 134, 69, 69, 55, 55, 42, 42, 42, 42, 38, 38, 10, 6, 6, 6, 6, 1, 5, 5, 5, 5, 6, 6] 201 rigid atoms, others: [48, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54]) total number of confs: 631 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113295 none C=CCCOCCCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 99, 90, 77, 60, 60, 54, 20, 20, 20, 15, 15, 15, 5, 5, 5, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 15, 201, 201, 201, 201, 201, 99, 99, 77, 77, 60, 60, 60, 60, 54, 54, 20, 15, 15, 15, 15, 5, 2, 2, 2, 2, 15, 15] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 896 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113295 none C=CCCOCCCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 88, 44, 35, 27, 18, 18, 16, 4, 4, 4, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 14, 6, 6, 1, 95, 95, 95, 88, 88, 44, 44, 27, 27, 18, 18, 18, 18, 16, 16, 4, 1, 1, 1, 1, 6, 14, 14, 14, 14, 1, 1] 201 rigid atoms, others: [47, 15, 12, 11, 44, 13, 14, 45, 46, 54, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50, 51, 52]) total number of confs: 463 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113295 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113295/1 /scratch/stefan/7770410/working/building/REAL300020113295 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 187) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/187 `/scratch/stefan/7770410/working/3D/187' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCOCCCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113295.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113295 none C=CCCOCCCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [137, 134, 69, 63, 55, 42, 42, 38, 10, 10, 10, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 6, 137, 137, 137, 134, 134, 69, 69, 55, 55, 42, 42, 42, 42, 38, 38, 10, 6, 6, 6, 6, 1, 5, 5, 5, 5, 6, 6] 201 rigid atoms, others: [48, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54]) total number of confs: 631 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113295 none C=CCCOCCCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 99, 91, 78, 61, 61, 55, 21, 21, 21, 16, 16, 16, 6, 6, 6, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 16, 201, 201, 201, 201, 201, 99, 99, 78, 78, 61, 61, 61, 61, 55, 55, 21, 16, 16, 16, 16, 6, 2, 2, 2, 2, 16, 16] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 892 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113295 none C=CCCOCCCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 88, 44, 35, 27, 18, 18, 16, 4, 4, 4, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 14, 6, 6, 1, 95, 95, 95, 88, 88, 44, 44, 27, 27, 18, 18, 18, 18, 16, 16, 4, 1, 1, 1, 1, 6, 14, 14, 14, 14, 1, 1] 201 rigid atoms, others: [47, 15, 12, 11, 44, 13, 14, 45, 46, 54, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50, 51, 52]) total number of confs: 463 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113295 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113295 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113295/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113295/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113295 Building REAL300020113296 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113296' /scratch/stefan/7770410/working/building/REAL300020113296 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113296 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113296/0 /scratch/stefan/7770410/working/building/REAL300020113296 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/188 `/scratch/stefan/7770410/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC(C2CC2)=N1) `REAL300020113296.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113296 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 26, 39, 39, 39, 39, 39, 8, 8, 1, 14, 14, 14, 29, 29, 14, 14, 14, 14, 5, 1, 1, 1, 1, 8, 26, 26, 39, 39, 1, 1, 29, 29, 29, 29, 29] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 42, 21, 41] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47]) total number of confs: 227 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113296 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 15, 15, 15, 29, 29, 29, 105, 105, 105, 160, 201, 201, 201, 201, 201, 105, 105, 29, 7, 1, 1, 1, 1, 7, 8, 8, 8, 15, 29, 29, 29, 29, 105, 160, 160, 201, 201, 29, 29, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 46, 47, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 726 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113296 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 27, 27, 27, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 65, 65, 65, 105, 105, 65, 65, 65, 65, 27, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 105, 105, 105, 105, 105] 201 rigid atoms, others: [36, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 294 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113296 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 65, 65, 65, 125, 161, 161, 161, 161, 161, 65, 65, 14, 1, 1, 1, 7, 7, 1, 2, 2, 2, 5, 14, 14, 14, 14, 65, 125, 125, 161, 161, 14, 14, 7, 7, 7, 7, 7] 201 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 612 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113296 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [161, 161, 85, 85, 85, 39, 39, 39, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 39, 161, 161, 161, 201, 201, 161, 161, 161, 161, 85, 39, 39, 39, 39, 8, 4, 4, 2, 2, 39, 39, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 548 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113296 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113296/1 /scratch/stefan/7770410/working/building/REAL300020113296 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 189) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/189 `/scratch/stefan/7770410/working/3D/189' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC(C2CC2)=N1) `REAL300020113296.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113296/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113296 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 26, 39, 39, 39, 39, 39, 8, 8, 1, 15, 15, 15, 31, 31, 15, 15, 15, 15, 6, 1, 1, 1, 1, 8, 26, 26, 39, 39, 1, 1, 31, 31, 31, 31, 31] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 42, 21, 41] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47]) total number of confs: 233 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113296 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 16, 16, 16, 31, 31, 31, 105, 105, 105, 160, 201, 201, 201, 201, 201, 105, 105, 31, 7, 1, 1, 1, 1, 7, 8, 8, 8, 16, 31, 31, 31, 31, 105, 160, 160, 201, 201, 31, 31, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 46, 47, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 730 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113296 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 28, 28, 28, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 67, 67, 67, 105, 105, 67, 67, 67, 67, 28, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 105, 105, 105, 105, 105] 201 rigid atoms, others: [36, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 291 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113296 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 67, 67, 67, 125, 161, 161, 161, 161, 161, 67, 67, 15, 1, 1, 1, 7, 7, 1, 2, 2, 2, 5, 15, 15, 15, 15, 67, 125, 125, 161, 161, 15, 15, 7, 7, 7, 7, 7] 201 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 609 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113296 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [161, 161, 85, 85, 85, 39, 39, 39, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 39, 161, 161, 161, 201, 201, 161, 161, 161, 161, 85, 39, 39, 39, 39, 8, 4, 4, 2, 2, 39, 39, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 549 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113296 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113296 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113296/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113296/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113296 Building REAL300020113297 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113297' /scratch/stefan/7770410/working/building/REAL300020113297 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113297 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113297/0 /scratch/stefan/7770410/working/building/REAL300020113297 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/190 `/scratch/stefan/7770410/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COC1CCOC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113297.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113297 none O=C(COC1CCOC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 12, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 19, 33, 42, 42, 42, 42, 1, 1, 1, 1, 1, 8, 8, 8, 25, 38, 39, 39, 39, 39, 8, 8, 1, 19, 19, 42, 42, 42, 42, 42, 42, 42, 6, 1, 1, 1, 1, 8, 25, 25, 38, 38, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 280 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113297 none O=C(COC1CCOC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 12, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 69, 90, 103, 103, 103, 103, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 69, 69, 103, 103, 103, 103, 103, 103, 103, 23, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 370 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113297 none O=C(COC1CCOC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 12, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 13, 4, 1, 1, 1, 1, 1, 1, 25, 25, 42, 42, 42, 103, 103, 103, 168, 201, 201, 201, 201, 201, 103, 103, 42, 13, 13, 1, 1, 1, 1, 1, 1, 1, 25, 42, 42, 42, 42, 103, 168, 168, 201, 201, 42, 42] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 742 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113297 none O=C(COC1CCOC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 12, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 165, 186, 201, 201, 201, 201, 39, 39, 39, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 39, 165, 165, 201, 201, 201, 201, 201, 201, 201, 75, 39, 39, 39, 39, 9, 5, 5, 3, 3, 39, 39] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 729 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113297 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113297/1 /scratch/stefan/7770410/working/building/REAL300020113297 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 191) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/191 `/scratch/stefan/7770410/working/3D/191' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COC1CCOC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113297.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113297 none O=C(COC1CCOC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 12, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 19, 33, 42, 42, 42, 42, 1, 1, 1, 1, 1, 8, 8, 8, 25, 38, 39, 39, 39, 39, 8, 8, 1, 19, 19, 42, 42, 42, 42, 42, 42, 42, 6, 1, 1, 1, 1, 8, 25, 25, 38, 38, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 280 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113297 none O=C(COC1CCOC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 12, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 69, 91, 103, 103, 103, 103, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 69, 69, 103, 103, 103, 103, 103, 103, 103, 23, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 368 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113297 none O=C(COC1CCOC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 12, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 13, 4, 1, 1, 1, 1, 1, 1, 25, 25, 42, 42, 42, 103, 103, 103, 168, 201, 201, 201, 201, 201, 103, 103, 42, 13, 13, 1, 1, 1, 1, 1, 1, 1, 25, 42, 42, 42, 42, 103, 168, 168, 201, 201, 42, 42] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 741 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113297 none O=C(COC1CCOC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 12, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 165, 186, 201, 201, 201, 201, 38, 38, 38, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 38, 165, 165, 201, 201, 201, 201, 201, 201, 201, 74, 38, 38, 38, 38, 9, 5, 5, 3, 3, 38, 38] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 731 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113297 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113297 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113297/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113297/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113297 Building REAL300020113298 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113298' /scratch/stefan/7770410/working/building/REAL300020113298 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113298 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113298/0 /scratch/stefan/7770410/working/building/REAL300020113298 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/192 `/scratch/stefan/7770410/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)NC(N)=O) `REAL300020113298.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113298 none CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 79, 33, 33, 33, 10, 10, 10, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 10, 104, 112, 112, 112, 104, 104, 104, 104, 79, 79, 33, 10, 10, 10, 10, 1, 8, 8, 10, 10, 10, 10, 112, 112, 112] 201 rigid atoms, others: [37, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 509 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113298 none CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 191, 133, 133, 133, 64, 64, 64, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 64, 201, 201, 201, 201, 201, 201, 201, 201, 191, 191, 133, 64, 64, 64, 64, 14, 6, 6, 4, 4, 64, 64, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 708 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113298 none CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 25, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 36, 50, 60, 60, 60, 60, 10, 10, 1, 35, 42, 42, 42, 35, 35, 35, 35, 25, 25, 6, 1, 1, 1, 1, 10, 36, 36, 50, 50, 1, 1, 42, 42, 42] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 42, 43, 21] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 395 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113298 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113298/1 /scratch/stefan/7770410/working/building/REAL300020113298 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 193) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/193 `/scratch/stefan/7770410/working/3D/193' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)NC(N)=O) `REAL300020113298.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113298 none CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 80, 34, 34, 34, 10, 10, 10, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 10, 105, 113, 113, 113, 105, 105, 105, 105, 80, 80, 34, 10, 10, 10, 10, 1, 8, 8, 10, 10, 10, 10, 113, 113, 113] 201 rigid atoms, others: [37, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 511 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113298 none CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 191, 134, 134, 134, 63, 63, 63, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 63, 201, 201, 201, 201, 201, 201, 201, 201, 191, 191, 134, 63, 63, 63, 63, 13, 6, 6, 4, 4, 63, 63, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 705 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113298 none CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 25, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 36, 50, 60, 60, 60, 60, 10, 10, 1, 35, 42, 42, 42, 35, 35, 35, 35, 25, 25, 6, 1, 1, 1, 1, 10, 36, 36, 50, 50, 1, 1, 42, 42, 42] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 42, 43, 21] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 395 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113298 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113298 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113298/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113298/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113298 Building REAL300020113299 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113299' /scratch/stefan/7770410/working/building/REAL300020113299 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113299 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113299/0 /scratch/stefan/7770410/working/building/REAL300020113299 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/194 `/scratch/stefan/7770410/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CO1) `REAL300020113299.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113299 none CC(C)(C)C1=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 8, 19, 19, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 43, 62, 78, 78, 78, 78, 13, 13, 1, 8, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 13, 43, 43, 62, 62, 1, 1, 8] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49]) total number of confs: 347 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113299 none CC(C)(C)C1=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 61, 118, 118, 61, 61, 55, 55, 55, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 14, 14, 14, 14, 1, 1, 13, 61, 61, 118, 118, 118, 118, 118, 118, 118, 118, 118, 55, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13, 61] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 479 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113299 none CC(C)(C)C1=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 61, 61, 61, 138, 180, 201, 201, 201, 201, 61, 61, 8, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 61, 138, 138, 180, 180, 8, 8, 1] 201 rigid atoms, others: [1, 4, 5, 6, 7, 49, 26, 27] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 745 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113299 none CC(C)(C)C1=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 198, 198, 198, 78, 78, 78, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 78, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 198, 78, 78, 78, 78, 14, 6, 6, 4, 4, 78, 78, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 546 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113299 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113299/1 /scratch/stefan/7770410/working/building/REAL300020113299 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 195) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/195 `/scratch/stefan/7770410/working/3D/195' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CO1) `REAL300020113299.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113299 none CC(C)(C)C1=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 8, 19, 19, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 43, 62, 78, 78, 78, 78, 13, 13, 1, 8, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 13, 43, 43, 62, 62, 1, 1, 8] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49]) total number of confs: 347 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113299 none CC(C)(C)C1=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 61, 118, 118, 61, 61, 55, 55, 55, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 14, 14, 14, 14, 1, 1, 13, 61, 61, 118, 118, 118, 118, 118, 118, 118, 118, 118, 55, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13, 61] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 479 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113299 none CC(C)(C)C1=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 61, 61, 61, 138, 180, 201, 201, 201, 201, 61, 61, 8, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 61, 138, 138, 180, 180, 8, 8, 1] 201 rigid atoms, others: [1, 4, 5, 6, 7, 49, 26, 27] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 745 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113299 none CC(C)(C)C1=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 198, 198, 198, 78, 78, 78, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 78, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 198, 78, 78, 78, 78, 14, 6, 6, 4, 4, 78, 78, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 546 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113299 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113299 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113299/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113299/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113299 Building REAL300020113300 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113300' /scratch/stefan/7770410/working/building/REAL300020113300 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113300 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113300/0 /scratch/stefan/7770410/working/building/REAL300020113300 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/196 `/scratch/stefan/7770410/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C(C(C)C)O1) `REAL300020113300.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113300 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C(C(C)C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 29, 44, 44, 44, 44, 44, 11, 11, 1, 14, 14, 14, 41, 41, 14, 14, 14, 14, 6, 1, 1, 1, 1, 11, 29, 29, 44, 44, 1, 1, 41, 41, 41, 41, 41, 41, 41] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 42, 21, 41] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 322 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113300 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C(C(C)C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 45, 45, 45, 11, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 11, 80, 80, 80, 130, 130, 80, 80, 80, 80, 45, 11, 11, 11, 11, 1, 5, 5, 7, 7, 11, 11, 130, 130, 130, 130, 130, 130, 130] 201 rigid atoms, others: [36, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 471 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113300 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C(C(C)C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 80, 80, 80, 150, 187, 187, 187, 187, 187, 80, 80, 14, 1, 1, 1, 9, 9, 1, 2, 2, 2, 4, 14, 14, 14, 14, 80, 150, 150, 187, 187, 14, 14, 9, 9, 9, 9, 10, 10, 10] 201 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 719 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113300 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C(C(C)C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [187, 187, 132, 132, 132, 42, 42, 42, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 42, 187, 187, 187, 201, 201, 187, 187, 187, 187, 132, 42, 42, 42, 42, 7, 4, 4, 2, 2, 42, 42, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 544 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113300 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113300/1 /scratch/stefan/7770410/working/building/REAL300020113300 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 197) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/197 `/scratch/stefan/7770410/working/3D/197' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C(C(C)C)O1) `REAL300020113300.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113300 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C(C(C)C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 29, 44, 44, 44, 44, 44, 11, 11, 1, 14, 14, 14, 41, 41, 14, 14, 14, 14, 6, 1, 1, 1, 1, 11, 29, 29, 44, 44, 1, 1, 41, 41, 41, 41, 41, 41, 41] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 42, 21, 41] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 322 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113300 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C(C(C)C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 45, 45, 45, 11, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 11, 79, 79, 79, 130, 130, 79, 79, 79, 79, 45, 11, 11, 11, 11, 1, 5, 5, 7, 7, 11, 11, 130, 130, 130, 130, 130, 130, 130] 201 rigid atoms, others: [36, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 472 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113300 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C(C(C)C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 79, 79, 79, 149, 186, 186, 186, 186, 186, 79, 79, 14, 1, 1, 1, 9, 9, 1, 2, 2, 2, 4, 14, 14, 14, 14, 79, 149, 149, 186, 186, 14, 14, 9, 9, 9, 9, 10, 10, 10] 201 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 718 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113300 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C(C(C)C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [187, 187, 132, 132, 132, 42, 42, 42, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 42, 187, 187, 187, 201, 201, 187, 187, 187, 187, 132, 42, 42, 42, 42, 7, 4, 4, 2, 2, 42, 42, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 544 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113300 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113300 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113300/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113300/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113300 Building REAL300020113301 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113301' /scratch/stefan/7770410/working/building/REAL300020113301 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113301 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113301/0 /scratch/stefan/7770410/working/building/REAL300020113301 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/198 `/scratch/stefan/7770410/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CN(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1=O) `REAL300020113301.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113301 none CC1=CC=CN(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 29, 27, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 29, 41, 42, 42, 42, 42, 9, 9, 1, 29, 29, 29, 29, 29, 29, 29, 29, 27, 27, 6, 1, 1, 1, 1, 9, 29, 29, 41, 41, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 259 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113301 none CC1=CC=CN(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 106, 106, 96, 28, 28, 28, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 9, 106, 106, 106, 106, 106, 106, 106, 106, 96, 96, 28, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 393 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113301 none CC1=CC=CN(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 11, 11, 11, 29, 29, 29, 106, 106, 106, 171, 201, 201, 201, 201, 201, 106, 106, 29, 1, 1, 2, 2, 2, 1, 1, 1, 3, 3, 11, 29, 29, 29, 29, 106, 171, 171, 201, 201, 29, 29] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 33, 26, 27, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 723 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113301 none CC1=CC=CN(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 191, 87, 87, 87, 44, 44, 44, 11, 11, 11, 5, 3, 1, 1, 1, 1, 1, 1, 11, 11, 44, 201, 201, 201, 201, 201, 201, 201, 201, 191, 191, 87, 44, 44, 44, 44, 11, 5, 5, 3, 3, 44, 44] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 730 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113301 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113301/1 /scratch/stefan/7770410/working/building/REAL300020113301 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 199) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/199 `/scratch/stefan/7770410/working/3D/199' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CN(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1=O) `REAL300020113301.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113301 none CC1=CC=CN(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 29, 27, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 28, 40, 42, 42, 42, 42, 9, 9, 1, 29, 29, 29, 29, 29, 29, 29, 29, 27, 27, 6, 1, 1, 1, 1, 9, 28, 28, 40, 40, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 258 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113301 none CC1=CC=CN(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 105, 105, 95, 28, 28, 28, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 9, 105, 105, 105, 105, 105, 105, 105, 105, 95, 95, 28, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 390 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113301 none CC1=CC=CN(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 11, 11, 11, 29, 29, 29, 105, 105, 105, 170, 201, 201, 201, 201, 201, 105, 105, 29, 1, 1, 2, 2, 2, 1, 1, 1, 3, 3, 11, 29, 29, 29, 29, 105, 170, 170, 201, 201, 29, 29] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 33, 26, 27, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 725 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113301 none CC1=CC=CN(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 191, 88, 88, 88, 43, 43, 43, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 43, 201, 201, 201, 201, 201, 201, 201, 201, 191, 191, 88, 43, 43, 43, 43, 10, 5, 5, 3, 3, 43, 43] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 731 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113301 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113301 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113301/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113301/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113301 Building REAL300020113302 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113302' /scratch/stefan/7770410/working/building/REAL300020113302 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113302 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113302/0 /scratch/stefan/7770410/working/building/REAL300020113302 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/200 `/scratch/stefan/7770410/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC=C1) `REAL300020113302.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113302 none CC1=C([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 29, 29, 29, 104, 104, 104, 143, 169, 169, 169, 169, 169, 104, 104, 29, 4, 4, 4, 4, 4, 4, 1, 1, 10, 29, 29, 29, 29, 104, 143, 143, 169, 169, 29, 29, 4, 4] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 34] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 525 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113302 none CC1=C([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 167, 167, 167, 167, 91, 167, 91, 91, 39, 39, 39, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 39, 201, 201, 201, 201, 201, 201, 167, 167, 91, 39, 39, 39, 39, 7, 4, 4, 2, 2, 39, 39, 201, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 566 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113302 none CC1=C([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 29, 29, 29, 29, 5, 29, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 28, 39, 39, 39, 39, 39, 10, 10, 1, 47, 47, 47, 47, 47, 47, 29, 29, 5, 1, 1, 1, 1, 10, 28, 28, 39, 39, 1, 1, 47, 47] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 258 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113302 none CC1=C([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 4, 4, 19, 19, 19, 47, 47, 47, 133, 133, 133, 174, 201, 201, 201, 201, 201, 133, 133, 47, 1, 1, 1, 2, 2, 2, 4, 4, 19, 47, 47, 47, 47, 133, 174, 174, 201, 201, 47, 47, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 47, 48, 27, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 623 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113302 none CC1=C([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 104, 104, 104, 104, 34, 104, 34, 34, 10, 10, 10, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 10, 133, 133, 133, 133, 133, 133, 104, 104, 34, 10, 10, 10, 10, 1, 5, 5, 7, 7, 10, 10, 133, 133] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 361 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113302 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113302/1 /scratch/stefan/7770410/working/building/REAL300020113302 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 201) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/201 `/scratch/stefan/7770410/working/3D/201' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC=C1) `REAL300020113302.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113302 none CC1=C([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 29, 29, 29, 104, 104, 104, 142, 168, 168, 168, 168, 168, 104, 104, 29, 4, 4, 4, 4, 4, 4, 1, 1, 10, 29, 29, 29, 29, 104, 142, 142, 168, 168, 29, 29, 4, 4] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 34] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 519 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113302 none CC1=C([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 168, 168, 168, 168, 91, 168, 91, 91, 39, 39, 39, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 39, 201, 201, 201, 201, 201, 201, 168, 168, 91, 39, 39, 39, 39, 7, 4, 4, 2, 2, 39, 39, 201, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 568 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113302 none CC1=C([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 29, 29, 29, 29, 5, 29, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 28, 39, 39, 39, 39, 39, 10, 10, 1, 47, 47, 47, 47, 47, 47, 29, 29, 5, 1, 1, 1, 1, 10, 28, 28, 39, 39, 1, 1, 47, 47] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 258 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113302 none CC1=C([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 4, 4, 19, 19, 19, 47, 47, 47, 134, 134, 134, 175, 201, 201, 201, 201, 201, 134, 134, 47, 1, 1, 1, 2, 2, 2, 4, 4, 19, 47, 47, 47, 47, 134, 175, 175, 201, 201, 47, 47, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 47, 48, 27, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 618 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113302 none CC1=C([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 104, 104, 104, 104, 34, 104, 34, 34, 10, 10, 10, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 10, 134, 134, 134, 134, 134, 134, 104, 104, 34, 10, 10, 10, 10, 1, 5, 5, 7, 7, 10, 10, 134, 134] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 363 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113302 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113302 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113302/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113302/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113302 Building REAL300020113303 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113303' /scratch/stefan/7770410/working/building/REAL300020113303 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113303 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113303/0 /scratch/stefan/7770410/working/building/REAL300020113303 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/202 `/scratch/stefan/7770410/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2N=CSC2=CC=C1) `REAL300020113303.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113303 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2N=CSC2=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 14, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 6, 20, 80, 80, 80, 80, 80, 80, 80, 80, 20, 6, 6, 6, 6, 1, 8, 8, 10, 10, 6, 6, 80, 80, 80, 80] 141 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 169 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113303 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2N=CSC2=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 14, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 40, 40, 40, 17, 17, 17, 7, 4, 1, 1, 1, 1, 1, 1, 17, 17, 40, 68, 140, 140, 140, 140, 140, 140, 140, 140, 68, 40, 40, 40, 40, 17, 7, 7, 4, 4, 40, 40, 140, 140, 140, 140] 140 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 310 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113303 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2N=CSC2=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 14, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 23, 32, 37, 37, 37, 37, 6, 6, 1, 6, 42, 42, 42, 42, 42, 42, 42, 42, 6, 1, 1, 1, 1, 6, 23, 23, 32, 32, 1, 1, 42, 42, 42, 42] 141 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 190 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113303 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2N=CSC2=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 14, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 42, 42, 42, 80, 80, 80, 131, 141, 141, 141, 141, 141, 80, 80, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 42, 42, 42, 42, 80, 131, 131, 141, 141, 42, 42, 1, 1, 1, 1] 141 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 494 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113303 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113303/1 /scratch/stefan/7770410/working/building/REAL300020113303 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 203) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/203 `/scratch/stefan/7770410/working/3D/203' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2N=CSC2=CC=C1) `REAL300020113303.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113303 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2N=CSC2=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 14, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 6, 20, 81, 81, 81, 81, 81, 81, 81, 81, 20, 6, 6, 6, 6, 1, 8, 8, 10, 10, 6, 6, 81, 81, 81, 81] 142 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 170 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113303 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2N=CSC2=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 14, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 40, 40, 40, 17, 17, 17, 7, 4, 1, 1, 1, 1, 1, 1, 17, 17, 40, 70, 142, 142, 142, 142, 142, 142, 142, 142, 70, 40, 40, 40, 40, 17, 7, 7, 4, 4, 40, 40, 142, 142, 142, 142] 142 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 316 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113303 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2N=CSC2=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 14, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 23, 32, 37, 37, 37, 37, 6, 6, 1, 6, 42, 42, 42, 42, 42, 42, 42, 42, 6, 1, 1, 1, 1, 6, 23, 23, 32, 32, 1, 1, 42, 42, 42, 42] 142 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 190 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113303 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2N=CSC2=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 14, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 42, 42, 42, 81, 81, 81, 132, 142, 142, 142, 142, 142, 81, 81, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 42, 42, 42, 42, 81, 132, 132, 142, 142, 42, 42, 1, 1, 1, 1] 142 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 495 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113303 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113303 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113303/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113303/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113303 Building REAL300020113304 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113304' /scratch/stefan/7770410/working/building/REAL300020113304 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113304 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113304/0 /scratch/stefan/7770410/working/building/REAL300020113304 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/204 `/scratch/stefan/7770410/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C(F)F)CC1) `REAL300020113304.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113304 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C(F)F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 15, 15, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 8, 31, 63, 77, 77, 63, 63, 31, 8, 8, 8, 8, 1, 3, 3, 3, 3, 8, 8, 77, 63, 63, 63, 63] 77 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 274 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113304 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C(F)F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 15, 15, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 41, 41, 41, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 41, 111, 180, 201, 201, 180, 180, 111, 41, 41, 41, 41, 10, 6, 6, 4, 4, 41, 41, 201, 180, 180, 180, 180] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 657 number of broken/clashed sets: 39 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113304 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C(F)F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 15, 15, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 9, 9, 9, 9, 9, 9, 8, 8, 1, 6, 20, 61, 61, 20, 20, 6, 1, 1, 1, 1, 8, 9, 9, 9, 9, 1, 1, 61, 20, 20, 20, 20] 77 rigid atoms, others: [2, 3, 4, 5, 6, 18, 35, 36, 26, 27, 28, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41]) total number of confs: 242 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113304 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C(F)F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 15, 15, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 20, 20, 20, 63, 63, 63, 64, 64, 64, 64, 64, 64, 63, 63, 20, 1, 1, 11, 11, 1, 1, 5, 20, 20, 20, 20, 63, 64, 64, 64, 64, 20, 20, 11, 1, 1, 1, 1] 77 rigid atoms, others: [1, 38, 39, 40, 41, 19, 20, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 149 number of broken/clashed sets: 19 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113304 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113304/1 /scratch/stefan/7770410/working/building/REAL300020113304 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 205) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/205 `/scratch/stefan/7770410/working/3D/205' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C(F)F)CC1) `REAL300020113304.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113304/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113304 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C(F)F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 15, 15, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 8, 31, 63, 77, 77, 63, 63, 31, 8, 8, 8, 8, 1, 3, 3, 3, 3, 8, 8, 77, 63, 63, 63, 63] 77 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 274 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113304 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C(F)F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 15, 15, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 42, 42, 42, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 42, 111, 180, 201, 201, 180, 180, 111, 42, 42, 42, 42, 10, 6, 6, 4, 4, 42, 42, 201, 180, 180, 180, 180] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 663 number of broken/clashed sets: 39 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113304 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C(F)F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 15, 15, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 9, 9, 9, 9, 9, 9, 8, 8, 1, 6, 20, 61, 61, 20, 20, 6, 1, 1, 1, 1, 8, 9, 9, 9, 9, 1, 1, 61, 20, 20, 20, 20] 77 rigid atoms, others: [2, 3, 4, 5, 6, 18, 35, 36, 26, 27, 28, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41]) total number of confs: 242 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113304 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C(F)F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 15, 15, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 20, 20, 20, 63, 63, 63, 64, 64, 64, 64, 64, 64, 63, 63, 20, 1, 1, 11, 11, 1, 1, 5, 20, 20, 20, 20, 63, 64, 64, 64, 64, 20, 20, 11, 1, 1, 1, 1] 77 rigid atoms, others: [1, 38, 39, 40, 41, 19, 20, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 149 number of broken/clashed sets: 19 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113304 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113304 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113304/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113304/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113304 Building REAL300020113305 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113305' /scratch/stefan/7770410/working/building/REAL300020113305 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113305 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113305/0 /scratch/stefan/7770410/working/building/REAL300020113305 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/206 `/scratch/stefan/7770410/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC2(CC2)C1) `REAL300020113305.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113305 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC2(CC2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 29, 92, 92, 92, 92, 92, 92, 92, 29, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 275 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113305 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC2(CC2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 51, 51, 51, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 51, 99, 201, 201, 201, 201, 201, 201, 201, 99, 51, 51, 51, 51, 11, 6, 6, 4, 4, 51, 51, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 607 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113305 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC2(CC2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 31, 45, 50, 50, 50, 50, 11, 11, 1, 5, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 1, 11, 31, 31, 45, 45, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113305 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC2(CC2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 7, 17, 17, 17, 92, 92, 92, 154, 201, 201, 201, 201, 201, 92, 92, 17, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 17, 92, 154, 154, 201, 201, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 746 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113305 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113305/1 /scratch/stefan/7770410/working/building/REAL300020113305 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 207) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/207 `/scratch/stefan/7770410/working/3D/207' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2(CC2)C1) `REAL300020113305.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113305 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2(CC2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 30, 92, 92, 92, 92, 92, 92, 92, 30, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 273 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113305 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2(CC2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 50, 50, 50, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 50, 99, 201, 201, 201, 201, 201, 201, 201, 99, 50, 50, 50, 50, 10, 6, 6, 4, 4, 50, 50, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 607 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113305 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2(CC2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 30, 44, 49, 49, 49, 49, 11, 11, 1, 6, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 11, 30, 30, 44, 44, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113305 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2(CC2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 8, 19, 19, 19, 92, 92, 92, 154, 201, 201, 201, 201, 201, 92, 92, 19, 1, 1, 1, 1, 1, 1, 1, 1, 8, 19, 19, 19, 19, 92, 154, 154, 201, 201, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 748 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113305 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113305 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113305/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113305/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113305 Building REAL300020113306 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113306' /scratch/stefan/7770410/working/building/REAL300020113306 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113306 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113306/0 /scratch/stefan/7770410/working/building/REAL300020113306 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/208 `/scratch/stefan/7770410/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C2=CC=CC=N2)CC1) `REAL300020113306.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113306 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C2=CC=CC=N2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 49, 135, 155, 155, 155, 155, 155, 135, 135, 49, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 155, 155, 155, 155, 135, 135, 135, 135] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 437 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113306 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C2=CC=CC=N2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 5, 17, 17, 44, 44, 44, 155, 155, 155, 191, 201, 201, 201, 201, 201, 155, 155, 44, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 44, 44, 44, 44, 155, 191, 191, 201, 201, 44, 44, 1, 1, 1, 1, 5, 5, 5, 5] 201 rigid atoms, others: [40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47]) total number of confs: 533 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113306 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C2=CC=CC=N2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 36, 36, 36, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 36, 99, 201, 201, 201, 201, 201, 201, 201, 201, 99, 36, 36, 36, 36, 9, 4, 4, 2, 2, 36, 36, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 599 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113306 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C2=CC=CC=N2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 27, 37, 37, 37, 37, 37, 13, 13, 1, 6, 30, 44, 44, 44, 44, 44, 30, 30, 6, 1, 1, 1, 1, 13, 27, 27, 37, 37, 1, 1, 44, 44, 44, 44, 30, 30, 30, 30] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113306 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C2=CC=CC=N2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 30, 30, 30, 135, 135, 135, 178, 200, 200, 200, 200, 200, 135, 135, 30, 1, 1, 5, 5, 5, 5, 5, 1, 1, 9, 30, 30, 30, 30, 135, 178, 178, 200, 200, 30, 30, 5, 5, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [1, 44, 45, 46, 47, 19, 20, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 584 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113306 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113306/1 /scratch/stefan/7770410/working/building/REAL300020113306 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 209) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/209 `/scratch/stefan/7770410/working/3D/209' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C2=CC=CC=N2)CC1) `REAL300020113306.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113306/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113306 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C2=CC=CC=N2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 49, 132, 154, 154, 154, 154, 154, 132, 132, 49, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 154, 154, 154, 154, 132, 132, 132, 132] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 431 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113306 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C2=CC=CC=N2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 5, 17, 17, 44, 44, 44, 154, 154, 154, 191, 201, 201, 201, 201, 201, 154, 154, 44, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 44, 44, 44, 44, 154, 191, 191, 201, 201, 44, 44, 1, 1, 1, 1, 5, 5, 5, 5] 201 rigid atoms, others: [40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47]) total number of confs: 538 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113306 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C2=CC=CC=N2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 37, 37, 37, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 37, 100, 201, 201, 201, 201, 201, 201, 201, 201, 100, 37, 37, 37, 37, 9, 4, 4, 2, 2, 37, 37, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 601 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113306 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C2=CC=CC=N2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 27, 36, 36, 36, 36, 36, 13, 13, 1, 6, 30, 44, 44, 44, 44, 44, 30, 30, 6, 1, 1, 1, 1, 13, 27, 27, 36, 36, 1, 1, 44, 44, 44, 44, 30, 30, 30, 30] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113306 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C2=CC=CC=N2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 30, 30, 30, 132, 132, 132, 178, 200, 200, 200, 200, 200, 132, 132, 30, 1, 1, 5, 5, 5, 5, 5, 1, 1, 9, 30, 30, 30, 30, 132, 178, 178, 200, 200, 30, 30, 5, 5, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [1, 44, 45, 46, 47, 19, 20, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 596 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113306 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113306 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113306/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113306/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113306 Building REAL300020113307 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113307' /scratch/stefan/7770410/working/building/REAL300020113307 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113307 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113307/0 /scratch/stefan/7770410/working/building/REAL300020113307 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/210 `/scratch/stefan/7770410/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN(C2CCC2)N=C1) `REAL300020113307.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113307 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN(C2CCC2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 5, 5, 5, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 5, 17, 35, 35, 35, 82, 82, 82, 35, 35, 17, 5, 5, 5, 5, 1, 6, 6, 8, 8, 5, 5, 35, 82, 82, 82, 82, 82, 82, 82, 35] 123 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 247 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113307 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN(C2CCC2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [27, 11, 27, 27, 60, 60, 60, 82, 82, 82, 112, 123, 123, 123, 123, 123, 82, 82, 60, 11, 11, 1, 1, 1, 1, 1, 11, 11, 27, 60, 60, 60, 60, 82, 112, 112, 123, 123, 60, 60, 11, 1, 1, 1, 1, 1, 1, 1, 11] 123 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48]) total number of confs: 405 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113307 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN(C2CCC2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 35, 35, 35, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 35, 53, 71, 71, 71, 114, 114, 114, 71, 71, 53, 35, 35, 35, 35, 14, 6, 6, 4, 4, 35, 35, 71, 114, 114, 114, 114, 114, 114, 114, 71] 114 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 348 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113307 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN(C2CCC2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 18, 26, 31, 31, 31, 31, 5, 5, 1, 6, 18, 18, 18, 60, 60, 60, 18, 18, 6, 1, 1, 1, 1, 5, 18, 18, 26, 26, 1, 1, 18, 60, 60, 60, 60, 60, 60, 60, 18] 123 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113307 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN(C2CCC2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 18, 18, 18, 35, 35, 35, 54, 65, 71, 71, 71, 71, 35, 35, 18, 1, 1, 1, 1, 11, 11, 11, 1, 1, 5, 18, 18, 18, 18, 35, 54, 54, 65, 65, 18, 18, 1, 11, 11, 11, 11, 11, 11, 11, 1] 123 rigid atoms, others: [1, 40, 48, 19, 20, 21, 22, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 252 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113307 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113307/1 /scratch/stefan/7770410/working/building/REAL300020113307 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 211) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/211 `/scratch/stefan/7770410/working/3D/211' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN(C2CCC2)N=C1) `REAL300020113307.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113307/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113307 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN(C2CCC2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 5, 5, 5, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 5, 17, 35, 35, 35, 83, 83, 83, 35, 35, 17, 5, 5, 5, 5, 1, 6, 6, 8, 8, 5, 5, 35, 83, 83, 83, 83, 83, 83, 83, 35] 124 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 249 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113307 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN(C2CCC2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [27, 11, 27, 27, 60, 60, 60, 83, 83, 83, 113, 124, 124, 124, 124, 124, 83, 83, 60, 11, 11, 1, 1, 1, 1, 1, 11, 11, 27, 60, 60, 60, 60, 83, 113, 113, 124, 124, 60, 60, 11, 1, 1, 1, 1, 1, 1, 1, 11] 124 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48]) total number of confs: 406 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113307 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN(C2CCC2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 34, 34, 34, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 34, 53, 72, 72, 72, 116, 116, 116, 72, 72, 53, 34, 34, 34, 34, 13, 6, 6, 4, 4, 34, 34, 72, 116, 116, 116, 116, 116, 116, 116, 72] 116 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 354 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113307 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN(C2CCC2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 18, 26, 31, 31, 31, 31, 5, 5, 1, 6, 18, 18, 18, 60, 60, 60, 18, 18, 6, 1, 1, 1, 1, 5, 18, 18, 26, 26, 1, 1, 18, 60, 60, 60, 60, 60, 60, 60, 18] 124 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113307 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN(C2CCC2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 18, 18, 18, 35, 35, 35, 54, 65, 71, 71, 71, 71, 35, 35, 18, 1, 1, 1, 1, 11, 11, 11, 1, 1, 5, 18, 18, 18, 18, 35, 54, 54, 65, 65, 18, 18, 1, 11, 11, 11, 11, 11, 11, 11, 1] 124 rigid atoms, others: [1, 40, 48, 19, 20, 21, 22, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 252 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113307 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113307 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113307/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113307/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113307 Building REAL300020113308 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113308' /scratch/stefan/7770410/working/building/REAL300020113308 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113308 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113308/0 /scratch/stefan/7770410/working/building/REAL300020113308 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/212 `/scratch/stefan/7770410/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN2N=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=C2N=C1) `REAL300020113308.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113308 none CC1=CN2N=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 65, 88, 106, 106, 106, 106, 13, 13, 1, 13, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 13, 65, 65, 88, 88, 1, 1, 13] 201 rigid atoms, others: [45, 35, 36, 37, 38, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46]) total number of confs: 401 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113308 none CC1=CN2N=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 84, 84, 84, 54, 54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 19, 19, 19, 19, 1, 1, 13, 84, 84, 84, 84, 84, 84, 84, 84, 54, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 84] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 250 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113308 none CC1=CN2N=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 84, 84, 84, 172, 201, 201, 201, 201, 201, 84, 84, 13, 1, 1, 1, 2, 2, 2, 1, 1, 4, 13, 13, 13, 13, 84, 172, 172, 201, 201, 13, 13, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 46, 33, 26, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 717 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113308 none CC1=CN2N=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 199, 199, 199, 107, 107, 107, 22, 22, 22, 6, 4, 1, 1, 1, 1, 1, 1, 22, 22, 107, 201, 201, 201, 201, 201, 201, 201, 201, 199, 107, 107, 107, 107, 22, 6, 6, 4, 4, 107, 107, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 544 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113308 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113308/1 /scratch/stefan/7770410/working/building/REAL300020113308 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 213) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/213 `/scratch/stefan/7770410/working/3D/213' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN2N=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=C2N=C1) `REAL300020113308.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113308/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113308 none CC1=CN2N=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 65, 88, 106, 106, 106, 106, 13, 13, 1, 13, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 13, 65, 65, 88, 88, 1, 1, 13] 201 rigid atoms, others: [45, 35, 36, 37, 38, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46]) total number of confs: 401 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113308 none CC1=CN2N=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 84, 84, 84, 54, 54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 19, 19, 19, 19, 1, 1, 13, 84, 84, 84, 84, 84, 84, 84, 84, 54, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 84] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 250 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113308 none CC1=CN2N=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 84, 84, 84, 172, 201, 201, 201, 201, 201, 84, 84, 13, 1, 1, 1, 2, 2, 2, 1, 1, 4, 13, 13, 13, 13, 84, 172, 172, 201, 201, 13, 13, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 46, 33, 26, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 717 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113308 none CC1=CN2N=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 199, 199, 199, 107, 107, 107, 22, 22, 22, 6, 4, 1, 1, 1, 1, 1, 1, 22, 22, 107, 201, 201, 201, 201, 201, 201, 201, 201, 199, 107, 107, 107, 107, 22, 6, 6, 4, 4, 107, 107, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 542 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113308 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113308 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113308/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113308/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113308 Building REAL300020113309 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113309' /scratch/stefan/7770410/working/building/REAL300020113309 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113309 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113309/0 /scratch/stefan/7770410/working/building/REAL300020113309 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/214 `/scratch/stefan/7770410/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(=O)N(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1) `REAL300020113309.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113309 none CC1=CC(=O)N(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 29, 27, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 28, 40, 42, 42, 42, 42, 8, 8, 1, 29, 29, 29, 29, 29, 29, 27, 27, 6, 1, 1, 1, 1, 8, 28, 28, 40, 40, 1, 1, 29, 29] 201 rigid atoms, others: [45, 35, 36, 37, 38, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47]) total number of confs: 260 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113309 none CC1=CC(=O)N(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 101, 101, 91, 29, 29, 29, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 101, 101, 101, 101, 101, 101, 91, 91, 29, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 101, 101] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 374 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113309 none CC1=CC(=O)N(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 29, 29, 29, 101, 101, 101, 168, 201, 201, 201, 201, 201, 101, 101, 29, 1, 1, 2, 2, 2, 1, 2, 2, 11, 29, 29, 29, 29, 101, 168, 168, 201, 201, 29, 29, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 46, 47, 26, 27, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 725 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113309 none CC1=CC(=O)N(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 191, 86, 86, 86, 42, 42, 42, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 42, 201, 201, 201, 201, 201, 201, 191, 191, 86, 42, 42, 42, 42, 9, 5, 5, 3, 3, 42, 42, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 731 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113309 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113309/1 /scratch/stefan/7770410/working/building/REAL300020113309 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 215) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/215 `/scratch/stefan/7770410/working/3D/215' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(=O)N(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1) `REAL300020113309.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113309 none CC1=CC(=O)N(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 29, 27, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 28, 40, 42, 42, 42, 42, 8, 8, 1, 29, 29, 29, 29, 29, 29, 27, 27, 6, 1, 1, 1, 1, 8, 28, 28, 40, 40, 1, 1, 29, 29] 201 rigid atoms, others: [45, 35, 36, 37, 38, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47]) total number of confs: 260 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113309 none CC1=CC(=O)N(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 100, 100, 90, 28, 28, 28, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 100, 100, 100, 100, 100, 100, 90, 90, 28, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 100, 100] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 372 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113309 none CC1=CC(=O)N(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 29, 29, 29, 100, 100, 100, 167, 201, 201, 201, 201, 201, 100, 100, 29, 1, 1, 2, 2, 2, 1, 2, 2, 11, 29, 29, 29, 29, 100, 167, 167, 201, 201, 29, 29, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 46, 47, 26, 27, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 730 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113309 none CC1=CC(=O)N(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 191, 86, 86, 86, 42, 42, 42, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 42, 201, 201, 201, 201, 201, 201, 191, 191, 86, 42, 42, 42, 42, 9, 5, 5, 3, 3, 42, 42, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 733 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113309 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113309 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113309/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113309/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113309 Building REAL300020113310 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113310' /scratch/stefan/7770410/working/building/REAL300020113310 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113310 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113310/0 /scratch/stefan/7770410/working/building/REAL300020113310 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/216 `/scratch/stefan/7770410/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CCCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=C1) `REAL300020113310.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113310 none CC1=NN(CCCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 34, 17, 28, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 17, 29, 30, 30, 30, 30, 7, 7, 1, 48, 48, 48, 48, 48, 48, 30, 29, 28, 28, 28, 28, 6, 1, 1, 1, 1, 7, 17, 17, 29, 29, 1, 1, 48, 48, 48, 48] 201 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 48, 49, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50, 51, 52, 53]) total number of confs: 330 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113310 none CC1=NN(CCCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 133, 114, 61, 100, 23, 23, 23, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 7, 133, 133, 133, 133, 133, 133, 104, 104, 100, 100, 100, 100, 23, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7, 133, 133, 133, 133] 201 rigid atoms, others: [43, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 696 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113310 none CC1=NN(CCCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 9, 13, 25, 25, 25, 48, 48, 48, 133, 133, 133, 172, 201, 201, 201, 201, 201, 133, 133, 48, 1, 1, 1, 2, 2, 2, 5, 5, 9, 9, 13, 13, 25, 48, 48, 48, 48, 133, 172, 172, 201, 201, 48, 48, 2, 2, 2, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 53, 26, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 701 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113310 none CC1=NN(CCCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 192, 118, 167, 55, 55, 55, 32, 32, 32, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 32, 201, 201, 201, 201, 201, 201, 178, 180, 167, 167, 167, 167, 55, 32, 32, 32, 32, 9, 5, 5, 3, 3, 32, 32, 201, 201, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 999 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113310 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113310/1 /scratch/stefan/7770410/working/building/REAL300020113310 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 217) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/217 `/scratch/stefan/7770410/working/3D/217' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CCCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=C1) `REAL300020113310.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113310 none CC1=NN(CCCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 34, 17, 28, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 17, 29, 30, 30, 30, 30, 7, 7, 1, 48, 48, 48, 48, 48, 48, 30, 29, 28, 28, 28, 28, 6, 1, 1, 1, 1, 7, 17, 17, 29, 29, 1, 1, 48, 48, 48, 48] 201 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 48, 49, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50, 51, 52, 53]) total number of confs: 330 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113310 none CC1=NN(CCCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 133, 115, 62, 101, 24, 24, 24, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 7, 133, 133, 133, 133, 133, 133, 105, 105, 101, 101, 101, 101, 24, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7, 133, 133, 133, 133] 201 rigid atoms, others: [43, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 696 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113310 none CC1=NN(CCCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 9, 13, 25, 25, 25, 48, 48, 48, 133, 133, 133, 172, 201, 201, 201, 201, 201, 133, 133, 48, 1, 1, 1, 2, 2, 2, 5, 5, 9, 9, 13, 13, 25, 48, 48, 48, 48, 133, 172, 172, 201, 201, 48, 48, 2, 2, 2, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 53, 26, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 700 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113310 none CC1=NN(CCCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 192, 119, 168, 56, 56, 56, 32, 32, 32, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 32, 201, 201, 201, 201, 201, 201, 178, 180, 168, 168, 168, 168, 56, 32, 32, 32, 32, 10, 5, 5, 3, 3, 32, 32, 201, 201, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 997 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113310 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113310 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113310/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113310/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113310 Building REAL300020113311 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113311' /scratch/stefan/7770410/working/building/REAL300020113311 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113311 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113311/0 /scratch/stefan/7770410/working/building/REAL300020113311 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/218 `/scratch/stefan/7770410/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(C2CC2)=NO1) `REAL300020113311.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113311 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(C2CC2)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 5, 5, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 13, 48, 52, 52, 52, 116, 116, 52, 52, 48, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 52, 116, 116, 116, 116, 116] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 357 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113311 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(C2CC2)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 5, 5, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 10, 14, 14, 35, 35, 35, 116, 116, 116, 175, 201, 201, 201, 201, 201, 116, 116, 35, 10, 10, 1, 1, 1, 1, 10, 10, 14, 35, 35, 35, 35, 116, 175, 175, 201, 201, 35, 35, 10, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 654 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113311 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(C2CC2)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 5, 5, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [136, 136, 53, 53, 53, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 53, 136, 136, 136, 136, 201, 201, 136, 136, 136, 53, 53, 53, 53, 9, 5, 5, 3, 3, 53, 53, 136, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 632 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113311 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(C2CC2)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 5, 5, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 37, 53, 54, 54, 54, 54, 13, 13, 1, 6, 8, 8, 8, 35, 35, 8, 8, 6, 1, 1, 1, 1, 13, 37, 37, 53, 53, 1, 1, 8, 35, 35, 35, 35, 35] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 298 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113311 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(C2CC2)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 5, 5, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 52, 52, 52, 104, 135, 136, 136, 136, 136, 52, 52, 8, 1, 1, 1, 1, 10, 10, 1, 1, 3, 8, 8, 8, 8, 52, 104, 104, 135, 135, 8, 8, 1, 10, 10, 10, 10, 10] 201 rigid atoms, others: [1, 39, 19, 20, 21, 22, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 517 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113311 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113311/1 /scratch/stefan/7770410/working/building/REAL300020113311 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 219) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/219 `/scratch/stefan/7770410/working/3D/219' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(C2CC2)=NO1) `REAL300020113311.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113311/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113311 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(C2CC2)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 5, 5, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 13, 48, 52, 52, 52, 116, 116, 52, 52, 48, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 52, 116, 116, 116, 116, 116] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 357 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113311 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(C2CC2)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 5, 5, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 10, 14, 14, 35, 35, 35, 116, 116, 116, 175, 201, 201, 201, 201, 201, 116, 116, 35, 10, 10, 1, 1, 1, 1, 10, 10, 14, 35, 35, 35, 35, 116, 175, 175, 201, 201, 35, 35, 10, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 654 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113311 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(C2CC2)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 5, 5, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [136, 136, 54, 54, 54, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 54, 136, 136, 136, 136, 201, 201, 136, 136, 136, 54, 54, 54, 54, 9, 5, 5, 3, 3, 54, 54, 136, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 630 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113311 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(C2CC2)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 5, 5, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 37, 53, 54, 54, 54, 54, 13, 13, 1, 6, 8, 8, 8, 35, 35, 8, 8, 6, 1, 1, 1, 1, 13, 37, 37, 53, 53, 1, 1, 8, 35, 35, 35, 35, 35] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 298 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113311 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(C2CC2)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 5, 5, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 52, 52, 52, 104, 135, 136, 136, 136, 136, 52, 52, 8, 1, 1, 1, 1, 10, 10, 1, 1, 3, 8, 8, 8, 8, 52, 104, 104, 135, 135, 8, 8, 1, 10, 10, 10, 10, 10] 201 rigid atoms, others: [1, 39, 19, 20, 21, 22, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 517 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113311 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113311 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113311/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113311/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113311 Building REAL300020113312 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113312' /scratch/stefan/7770410/working/building/REAL300020113312 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113312 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113312/0 /scratch/stefan/7770410/working/building/REAL300020113312 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/220 `/scratch/stefan/7770410/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=NO1) `REAL300020113312.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113312 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 46, 54, 54, 54, 54, 11, 11, 1, 21, 21, 21, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 11, 31, 31, 46, 46, 1, 1, 21] 201 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43]) total number of confs: 272 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113312 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 82, 82, 40, 40, 40, 11, 11, 11, 1, 1, 1, 1, 1, 5, 7, 10, 10, 10, 10, 1, 1, 11, 82, 82, 82, 108, 108, 108, 108, 108, 40, 11, 11, 11, 11, 1, 5, 5, 7, 7, 11, 11, 82] 201 rigid atoms, others: [36, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 322 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113312 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 7, 7, 7, 21, 21, 21, 82, 82, 82, 146, 189, 199, 199, 199, 199, 82, 82, 21, 1, 1, 1, 3, 4, 4, 3, 3, 7, 21, 21, 21, 21, 82, 146, 146, 189, 189, 21, 21, 1] 201 rigid atoms, others: [1, 2, 3, 4, 43, 23, 24, 25] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 731 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113312 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 199, 136, 136, 136, 55, 55, 55, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 55, 199, 199, 199, 201, 201, 201, 201, 201, 136, 55, 55, 55, 55, 11, 6, 6, 4, 4, 55, 55, 199] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 488 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113312 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113312/1 /scratch/stefan/7770410/working/building/REAL300020113312 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 221) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/221 `/scratch/stefan/7770410/working/3D/221' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=NO1) `REAL300020113312.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113312/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113312 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 46, 54, 54, 54, 54, 11, 11, 1, 21, 21, 21, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 11, 31, 31, 46, 46, 1, 1, 21] 201 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43]) total number of confs: 272 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113312 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 82, 82, 40, 40, 40, 11, 11, 11, 1, 1, 1, 1, 1, 5, 7, 10, 10, 10, 10, 1, 1, 11, 82, 82, 82, 108, 108, 108, 108, 108, 40, 11, 11, 11, 11, 1, 5, 5, 7, 7, 11, 11, 82] 201 rigid atoms, others: [36, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 319 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113312 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 7, 7, 7, 21, 21, 21, 82, 82, 82, 147, 189, 199, 199, 199, 199, 82, 82, 21, 1, 1, 1, 3, 4, 4, 3, 3, 7, 21, 21, 21, 21, 82, 147, 147, 189, 189, 21, 21, 1] 201 rigid atoms, others: [1, 2, 3, 4, 43, 23, 24, 25] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 728 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113312 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 199, 136, 136, 136, 55, 55, 55, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 55, 199, 199, 199, 201, 201, 201, 201, 201, 136, 55, 55, 55, 55, 11, 6, 6, 4, 4, 55, 55, 199] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 490 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113312 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113312 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113312/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113312/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113312 Building REAL300020113313 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113313' /scratch/stefan/7770410/working/building/REAL300020113313 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113313 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113313/0 /scratch/stefan/7770410/working/building/REAL300020113313 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/222 `/scratch/stefan/7770410/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CC=CS1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113313.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113313 none CC(CC1=CC=CS1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 14, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 26, 33, 33, 33, 33, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 29, 43, 46, 46, 46, 46, 10, 10, 1, 15, 15, 15, 15, 26, 26, 33, 33, 33, 6, 1, 1, 1, 1, 10, 29, 29, 43, 43, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 307 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113313 none CC(CC1=CC=CS1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 14, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 28, 62, 94, 113, 113, 113, 113, 28, 28, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 10, 62, 62, 62, 62, 94, 94, 113, 113, 113, 28, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 488 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113313 none CC(CC1=CC=CS1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 14, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 3, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 33, 33, 33, 113, 113, 113, 169, 201, 201, 201, 201, 201, 113, 113, 33, 6, 6, 6, 6, 3, 3, 1, 1, 1, 15, 33, 33, 33, 33, 113, 169, 169, 201, 201, 33, 33] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 35] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 695 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113313 none CC(CC1=CC=CS1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 14, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [153, 87, 153, 179, 201, 201, 201, 201, 87, 87, 46, 46, 46, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 46, 153, 153, 153, 153, 179, 179, 201, 201, 201, 87, 46, 46, 46, 46, 10, 6, 6, 4, 4, 46, 46] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 759 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113313 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113313/1 /scratch/stefan/7770410/working/building/REAL300020113313 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 223) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/223 `/scratch/stefan/7770410/working/3D/223' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CC=CS1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113313.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113313/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113313 none CC(CC1=CC=CS1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 14, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 26, 33, 33, 33, 33, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 30, 44, 47, 47, 47, 47, 11, 11, 1, 15, 15, 15, 15, 26, 26, 33, 33, 33, 6, 1, 1, 1, 1, 11, 30, 30, 44, 44, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 308 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113313 none CC(CC1=CC=CS1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 14, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 29, 63, 95, 114, 114, 114, 114, 29, 29, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 63, 63, 63, 63, 95, 95, 114, 114, 114, 29, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 490 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113313 none CC(CC1=CC=CS1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 14, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 3, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 33, 33, 33, 114, 114, 114, 169, 201, 201, 201, 201, 201, 114, 114, 33, 6, 6, 6, 6, 3, 3, 1, 1, 1, 15, 33, 33, 33, 33, 114, 169, 169, 201, 201, 33, 33] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 35] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 689 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113313 none CC(CC1=CC=CS1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 14, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [153, 86, 153, 179, 201, 201, 201, 201, 86, 86, 48, 48, 48, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 48, 153, 153, 153, 153, 179, 179, 201, 201, 201, 86, 48, 48, 48, 48, 11, 6, 6, 4, 4, 48, 48] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 754 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113313 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113313 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113313/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113313/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113313 Building REAL300020113314 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113314' /scratch/stefan/7770410/working/building/REAL300020113314 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300020113314 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113314/0 /scratch/stefan/7770410/working/building/REAL300020113314 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/224 `/scratch/stefan/7770410/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NC=CN1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113314.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113314 none CC(C)C1=NC=CN1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 33, 54, 33, 33, 33, 33, 21, 4, 4, 4, 1, 1, 1, 1, 1, 9, 9, 9, 24, 36, 36, 36, 36, 36, 9, 9, 1, 54, 54, 54, 54, 54, 54, 54, 33, 33, 21, 21, 4, 1, 1, 1, 1, 9, 24, 24, 36, 36, 1, 1] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 346 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113314 none CC(C)C1=NC=CN1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 109, 139, 109, 109, 109, 109, 77, 17, 17, 17, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 9, 139, 139, 139, 139, 139, 139, 139, 109, 109, 77, 77, 17, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 529 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113314 none CC(C)C1=NC=CN1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 21, 21, 21, 33, 33, 33, 109, 109, 109, 163, 201, 201, 201, 201, 201, 109, 109, 33, 4, 4, 4, 3, 4, 3, 3, 1, 1, 5, 5, 21, 33, 33, 33, 33, 109, 163, 163, 201, 201, 33, 33] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 35, 36] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 725 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113314 none CC(C)C1=NC=CN1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 171, 55, 55, 55, 34, 34, 34, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 34, 201, 201, 201, 201, 201, 201, 201, 201, 201, 171, 171, 55, 34, 34, 34, 34, 8, 4, 4, 2, 2, 34, 34] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 696 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113314 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113314/1 /scratch/stefan/7770410/working/building/REAL300020113314 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 225) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/225 `/scratch/stefan/7770410/working/3D/225' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NC=CN1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113314.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113314/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113314 none CC(C)C1=NC=CN1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 34, 54, 34, 34, 34, 34, 22, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 24, 36, 36, 36, 36, 36, 9, 9, 1, 54, 54, 54, 54, 54, 54, 54, 34, 34, 22, 22, 5, 1, 1, 1, 1, 9, 24, 24, 36, 36, 1, 1] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 342 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113314 none CC(C)C1=NC=CN1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 110, 139, 110, 110, 110, 110, 78, 18, 18, 18, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 9, 139, 139, 139, 139, 139, 139, 139, 110, 110, 78, 78, 18, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 528 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113314 none CC(C)C1=NC=CN1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 21, 21, 21, 34, 34, 34, 110, 110, 110, 164, 201, 201, 201, 201, 201, 110, 110, 34, 4, 4, 4, 3, 4, 3, 3, 1, 1, 5, 5, 21, 34, 34, 34, 34, 110, 164, 164, 201, 201, 34, 34] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 35, 36] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 721 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113314 none CC(C)C1=NC=CN1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 171, 55, 55, 55, 34, 34, 34, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 34, 201, 201, 201, 201, 201, 201, 201, 201, 201, 171, 171, 55, 34, 34, 34, 34, 8, 4, 4, 2, 2, 34, 34] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 690 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113314 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `2' /scratch/stefan/7770410/working/building/REAL300020113314/2 /scratch/stefan/7770410/working/building/REAL300020113314 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 2 (index: 226) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/226 `/scratch/stefan/7770410/working/3D/226' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=[NH+]C=CN1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113314.mol2' -> `2.mol2' `temp.mol2' -> `REAL300020113314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113314/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113314 none CC(C)C1=[NH+]C=CN1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 6, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [97, 68, 97, 68, 68, 68, 68, 68, 31, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 11, 11, 11, 11, 11, 11, 9, 9, 1, 97, 97, 97, 97, 97, 97, 97, 68, 68, 31, 31, 6, 1, 1, 1, 1, 9, 11, 11, 11, 11, 1, 1] 179 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 349 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113314 none CC(C)C1=[NH+]C=CN1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 6, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [177, 176, 177, 176, 176, 176, 176, 176, 105, 29, 29, 29, 9, 9, 9, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 9, 177, 177, 177, 177, 177, 177, 177, 176, 176, 105, 105, 29, 9, 9, 9, 9, 1, 5, 5, 5, 5, 9, 9] 179 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 511 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113314 none CC(C)C1=[NH+]C=CN1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 6, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 6, 22, 22, 22, 68, 68, 68, 176, 176, 176, 179, 179, 179, 179, 179, 179, 176, 176, 68, 4, 4, 4, 4, 4, 4, 4, 1, 1, 6, 6, 22, 68, 68, 68, 68, 176, 179, 179, 179, 179, 68, 68] 179 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 36, 37] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 369 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113314 none CC(C)C1=[NH+]C=CN1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 6, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [175, 175, 175, 175, 175, 175, 175, 175, 127, 45, 45, 45, 18, 18, 18, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 175, 175, 175, 175, 175, 175, 175, 175, 175, 127, 127, 45, 18, 18, 18, 18, 5, 3, 3, 1, 1, 18, 18] 175 rigid atoms, others: [48, 49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51]) total number of confs: 545 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113314 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113314 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 2: /scratch/stefan/7770410/working/building/REAL300020113314/2.* 1: /scratch/stefan/7770410/working/building/REAL300020113314/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113314/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113314 Building REAL300020113315 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113315' /scratch/stefan/7770410/working/building/REAL300020113315 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113315 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113315/0 /scratch/stefan/7770410/working/building/REAL300020113315 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/227 `/scratch/stefan/7770410/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(=O)N1) `REAL300020113315.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113315 none CC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 36, 47, 36, 36, 36, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 36, 46, 67, 67, 67, 67, 7, 7, 1, 36, 36, 36, 47, 47, 47, 47, 47, 47, 47, 36, 36, 6, 1, 1, 1, 1, 7, 36, 36, 46, 46, 1, 1, 36] 201 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 48, 49, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50]) total number of confs: 328 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113315 none CC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 80, 104, 80, 80, 80, 26, 26, 26, 7, 7, 7, 1, 1, 1, 1, 1, 8, 10, 17, 17, 17, 17, 1, 1, 7, 80, 80, 80, 104, 104, 104, 104, 104, 104, 104, 80, 80, 26, 7, 7, 7, 7, 1, 8, 8, 10, 10, 7, 7, 80] 201 rigid atoms, others: [43, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 331 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113315 none CC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 12, 12, 12, 36, 36, 36, 80, 80, 80, 170, 188, 201, 201, 201, 201, 80, 80, 36, 1, 1, 1, 3, 3, 3, 2, 3, 3, 3, 1, 1, 12, 36, 36, 36, 36, 80, 170, 170, 188, 188, 36, 36, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 50, 36, 26, 27, 28, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 721 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113315 none CC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 163, 163, 163, 76, 76, 76, 25, 25, 25, 7, 4, 1, 1, 1, 1, 1, 1, 25, 25, 76, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 163, 76, 76, 76, 76, 25, 7, 7, 4, 4, 76, 76, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 543 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113315 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113315/1 /scratch/stefan/7770410/working/building/REAL300020113315 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 228) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/228 `/scratch/stefan/7770410/working/3D/228' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(=O)N1) `REAL300020113315.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113315 none CC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 36, 46, 36, 36, 36, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 36, 46, 67, 67, 67, 67, 7, 7, 1, 36, 36, 36, 46, 46, 46, 46, 46, 46, 46, 36, 36, 6, 1, 1, 1, 1, 7, 36, 36, 46, 46, 1, 1, 36] 201 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 48, 49, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50]) total number of confs: 322 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113315 none CC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 81, 105, 81, 81, 81, 26, 26, 26, 7, 7, 7, 1, 1, 1, 1, 1, 8, 10, 17, 17, 17, 17, 1, 1, 7, 81, 81, 81, 105, 105, 105, 105, 105, 105, 105, 81, 81, 26, 7, 7, 7, 7, 1, 8, 8, 10, 10, 7, 7, 81] 201 rigid atoms, others: [43, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 333 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113315 none CC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 12, 12, 12, 36, 36, 36, 81, 81, 81, 170, 188, 201, 201, 201, 201, 81, 81, 36, 1, 1, 1, 3, 3, 3, 2, 3, 3, 3, 1, 1, 12, 36, 36, 36, 36, 81, 170, 170, 188, 188, 36, 36, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 50, 36, 26, 27, 28, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 719 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113315 none CC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 163, 163, 163, 76, 76, 76, 25, 25, 25, 7, 4, 1, 1, 1, 1, 1, 1, 25, 25, 76, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 163, 76, 76, 76, 76, 25, 7, 7, 4, 4, 76, 76, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 541 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113315 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113315 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113315/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113315/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113315 Building REAL300020113316 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113316' /scratch/stefan/7770410/working/building/REAL300020113316 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113316 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113316/0 /scratch/stefan/7770410/working/building/REAL300020113316 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/229 `/scratch/stefan/7770410/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C(C2CC2)N=C1) `REAL300020113316.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113316 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C(C2CC2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 24, 56, 56, 37, 56, 124, 124, 56, 56, 24, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 56, 124, 124, 124, 124, 124, 56] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 446 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113316 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C(C2CC2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 4, 22, 22, 40, 40, 40, 124, 124, 124, 178, 201, 201, 201, 201, 201, 124, 124, 40, 1, 11, 11, 1, 1, 1, 1, 11, 11, 22, 40, 40, 40, 40, 124, 178, 178, 201, 201, 40, 40, 11, 1, 1, 1, 1, 1, 11] 201 rigid atoms, others: [41, 42, 43, 44, 45, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46]) total number of confs: 674 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113316 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C(C2CC2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 43, 43, 43, 11, 11, 11, 6, 3, 1, 1, 1, 1, 1, 1, 11, 11, 43, 75, 146, 146, 120, 146, 201, 201, 146, 146, 75, 43, 43, 43, 43, 11, 6, 6, 3, 3, 43, 43, 146, 201, 201, 201, 201, 201, 146] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 687 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113316 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C(C2CC2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 26, 40, 41, 41, 41, 41, 8, 8, 1, 5, 12, 12, 8, 12, 40, 40, 12, 12, 5, 1, 1, 1, 1, 8, 26, 26, 40, 40, 1, 1, 12, 40, 40, 40, 40, 40, 12] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 284 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113316 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C(C2CC2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 12, 12, 12, 56, 56, 56, 110, 146, 147, 147, 147, 147, 56, 56, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 12, 12, 12, 12, 56, 110, 110, 146, 146, 12, 12, 1, 11, 11, 11, 11, 11, 1] 201 rigid atoms, others: [1, 40, 46, 19, 20, 21, 22, 23, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 590 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113316 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113316/1 /scratch/stefan/7770410/working/building/REAL300020113316 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 230) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/230 `/scratch/stefan/7770410/working/3D/230' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C(C2CC2)N=C1) `REAL300020113316.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113316/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113316 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C(C2CC2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 24, 56, 56, 37, 56, 124, 124, 56, 56, 24, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 56, 124, 124, 124, 124, 124, 56] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 448 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113316 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C(C2CC2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 4, 23, 23, 40, 40, 40, 124, 124, 124, 178, 201, 201, 201, 201, 201, 124, 124, 40, 1, 11, 11, 1, 1, 1, 1, 11, 11, 23, 40, 40, 40, 40, 124, 178, 178, 201, 201, 40, 40, 11, 1, 1, 1, 1, 1, 11] 201 rigid atoms, others: [41, 42, 43, 44, 45, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46]) total number of confs: 672 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113316 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C(C2CC2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 45, 45, 45, 12, 12, 12, 7, 4, 1, 1, 1, 1, 1, 1, 12, 12, 45, 77, 148, 148, 122, 148, 201, 201, 148, 148, 77, 45, 45, 45, 45, 12, 7, 7, 4, 4, 45, 45, 148, 201, 201, 201, 201, 201, 148] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 684 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113316 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C(C2CC2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 26, 40, 41, 41, 41, 41, 8, 8, 1, 5, 12, 12, 8, 12, 40, 40, 12, 12, 5, 1, 1, 1, 1, 8, 26, 26, 40, 40, 1, 1, 12, 40, 40, 40, 40, 40, 12] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 284 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113316 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C(C2CC2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 12, 12, 12, 56, 56, 56, 109, 145, 147, 147, 147, 147, 56, 56, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 12, 12, 12, 12, 56, 109, 109, 145, 145, 12, 12, 1, 11, 11, 11, 11, 11, 1] 201 rigid atoms, others: [1, 40, 46, 19, 20, 21, 22, 23, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 589 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113316 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113316 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113316/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113316/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113316 Building REAL300020113317 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113317' /scratch/stefan/7770410/working/building/REAL300020113317 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113317 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113317/0 /scratch/stefan/7770410/working/building/REAL300020113317 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/231 `/scratch/stefan/7770410/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(C)C)=NC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113317.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113317 none CC1=NC(C(C)C)=NC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 10, 18, 39, 39, 23, 23, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 25, 38, 39, 39, 39, 39, 8, 8, 1, 23, 23, 23, 39, 39, 39, 39, 39, 39, 39, 23, 6, 1, 1, 1, 1, 8, 25, 25, 38, 38, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 334 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113317 none CC1=NC(C(C)C)=NC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 39, 69, 120, 120, 95, 95, 24, 24, 24, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 95, 95, 95, 120, 120, 120, 120, 120, 120, 120, 95, 24, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 587 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113317 none CC1=NC(C(C)C)=NC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 8, 8, 8, 23, 23, 23, 95, 95, 95, 155, 200, 201, 201, 201, 201, 95, 95, 23, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 1, 8, 23, 23, 23, 23, 95, 155, 155, 200, 200, 23, 23] 201 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 39] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 749 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113317 none CC1=NC(C(C)C)=NC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 131, 190, 201, 201, 201, 201, 78, 78, 78, 40, 40, 40, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 40, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 78, 40, 40, 40, 40, 10, 6, 6, 4, 4, 40, 40] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 746 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113317 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113317/1 /scratch/stefan/7770410/working/building/REAL300020113317 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 232) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/232 `/scratch/stefan/7770410/working/3D/232' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(C)C)=NC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113317.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113317 none CC1=NC(C(C)C)=NC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 10, 18, 39, 39, 23, 23, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 25, 38, 40, 40, 40, 40, 8, 8, 1, 23, 23, 23, 39, 39, 39, 39, 39, 39, 39, 23, 6, 1, 1, 1, 1, 8, 25, 25, 38, 38, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 336 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113317 none CC1=NC(C(C)C)=NC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 39, 69, 119, 119, 95, 95, 24, 24, 24, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 8, 95, 95, 95, 119, 119, 119, 119, 119, 119, 119, 95, 24, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 583 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113317 none CC1=NC(C(C)C)=NC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 8, 8, 8, 23, 23, 23, 95, 95, 95, 154, 199, 201, 201, 201, 201, 95, 95, 23, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 1, 8, 23, 23, 23, 23, 95, 154, 154, 199, 199, 23, 23] 201 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 39] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 745 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113317 none CC1=NC(C(C)C)=NC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 131, 189, 201, 201, 201, 201, 78, 78, 78, 41, 41, 41, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 41, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 78, 41, 41, 41, 41, 11, 6, 6, 4, 4, 41, 41] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 744 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113317 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113317 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113317/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113317/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113317 Building REAL300020113318 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113318' /scratch/stefan/7770410/working/building/REAL300020113318 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113318 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113318/0 /scratch/stefan/7770410/working/building/REAL300020113318 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/233 `/scratch/stefan/7770410/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CSC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113318.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113318 none O=C(CC1=CSC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 9, 9, 9, 32, 47, 55, 55, 55, 55, 9, 9, 1, 27, 27, 27, 27, 6, 1, 1, 1, 1, 9, 32, 32, 47, 47, 1, 1] 201 rigid atoms, others: [32, 33, 39, 8, 9, 10, 11, 12, 40, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38]) total number of confs: 296 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113318 none O=C(CC1=CSC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 105, 105, 105, 105, 105, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 105, 105, 105, 105, 31, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9] 201 rigid atoms, others: [34, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 404 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113318 none O=C(CC1=CSC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 3, 1, 1, 1, 1, 1, 1, 9, 9, 27, 27, 27, 105, 105, 105, 167, 201, 201, 201, 201, 201, 105, 105, 27, 3, 3, 1, 1, 9, 27, 27, 27, 27, 105, 167, 167, 201, 201, 27, 27] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 702 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113318 none O=C(CC1=CSC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 111, 201, 201, 201, 201, 201, 55, 55, 55, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 55, 201, 201, 201, 201, 111, 55, 55, 55, 55, 11, 6, 6, 4, 4, 55, 55] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 749 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113318 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113318/1 /scratch/stefan/7770410/working/building/REAL300020113318 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 234) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/234 `/scratch/stefan/7770410/working/3D/234' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CSC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113318.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113318 none O=C(CC1=CSC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 9, 9, 9, 31, 46, 54, 54, 54, 54, 9, 9, 1, 27, 27, 27, 27, 6, 1, 1, 1, 1, 9, 31, 31, 46, 46, 1, 1] 201 rigid atoms, others: [32, 33, 39, 8, 9, 10, 11, 12, 40, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38]) total number of confs: 293 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113318 none O=C(CC1=CSC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 105, 105, 105, 105, 105, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 105, 105, 105, 105, 31, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9] 201 rigid atoms, others: [34, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 404 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113318 none O=C(CC1=CSC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 3, 1, 1, 1, 1, 1, 1, 9, 9, 27, 27, 27, 105, 105, 105, 167, 201, 201, 201, 201, 201, 105, 105, 27, 3, 3, 1, 1, 9, 27, 27, 27, 27, 105, 167, 167, 201, 201, 27, 27] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 702 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113318 none O=C(CC1=CSC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 201, 201, 201, 201, 201, 57, 57, 57, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 57, 201, 201, 201, 201, 112, 57, 57, 57, 57, 13, 6, 6, 4, 4, 57, 57] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 743 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113318 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113318 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113318/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113318/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113318 Building REAL300020113319 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113319' /scratch/stefan/7770410/working/building/REAL300020113319 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113319 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113319/0 /scratch/stefan/7770410/working/building/REAL300020113319 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/235 `/scratch/stefan/7770410/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCN(C(=O)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1) `REAL300020113319.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113319 none CC1CCN(C(=O)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 11, 6, 15, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 28, 42, 42, 42, 42, 42, 9, 9, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 9, 28, 28, 42, 42, 1, 1, 29, 29, 29, 29] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 236 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113319 none CC1CCN(C(=O)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 116, 116, 62, 30, 74, 30, 30, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 9, 116, 116, 116, 116, 116, 116, 116, 116, 116, 116, 30, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 116, 116, 116, 116] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 319 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113319 none CC1CCN(C(=O)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 11, 11, 11, 29, 29, 29, 116, 116, 116, 175, 201, 201, 201, 201, 201, 116, 116, 29, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 11, 29, 29, 29, 29, 116, 175, 175, 201, 201, 29, 29, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 51, 32, 5, 34, 48, 49, 50, 35, 26, 27, 28, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 670 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113319 none CC1CCN(C(=O)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 159, 90, 165, 90, 90, 43, 43, 43, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 43, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 90, 43, 43, 43, 43, 9, 4, 4, 2, 2, 43, 43, 201, 201, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 564 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113319 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113319/1 /scratch/stefan/7770410/working/building/REAL300020113319 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 236) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/236 `/scratch/stefan/7770410/working/3D/236' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCN(C(=O)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1) `REAL300020113319.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113319/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113319 none CC1CCN(C(=O)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 11, 6, 15, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 28, 42, 42, 42, 42, 42, 9, 9, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 9, 28, 28, 42, 42, 1, 1, 29, 29, 29, 29] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 236 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113319 none CC1CCN(C(=O)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 116, 116, 62, 30, 74, 30, 30, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 9, 116, 116, 116, 116, 116, 116, 116, 116, 116, 116, 30, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 116, 116, 116, 116] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 319 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113319 none CC1CCN(C(=O)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 11, 11, 11, 29, 29, 29, 116, 116, 116, 174, 201, 201, 201, 201, 201, 116, 116, 29, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 11, 29, 29, 29, 29, 116, 174, 174, 201, 201, 29, 29, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 51, 32, 5, 34, 48, 49, 50, 35, 26, 27, 28, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 673 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113319 none CC1CCN(C(=O)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 158, 89, 164, 89, 89, 43, 43, 43, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 43, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 89, 43, 43, 43, 43, 9, 4, 4, 2, 2, 43, 43, 201, 201, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 563 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113319 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113319 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113319/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113319/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113319 Building REAL300020113320 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113320' /scratch/stefan/7770410/working/building/REAL300020113320 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113320 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113320/0 /scratch/stefan/7770410/working/building/REAL300020113320 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/237 `/scratch/stefan/7770410/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCN(C(=O)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1) `REAL300020113320.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113320 none CC1CCCN(C(=O)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 33, 18, 6, 19, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 26, 34, 34, 34, 34, 34, 13, 13, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 6, 1, 1, 1, 1, 13, 26, 26, 34, 34, 1, 1, 33, 33] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50, 51]) total number of confs: 203 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113320 none CC1CCCN(C(=O)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [154, 154, 154, 154, 154, 103, 58, 103, 58, 58, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 13, 154, 154, 154, 154, 154, 154, 154, 154, 154, 154, 154, 58, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 154, 154] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 426 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113320 none CC1CCCN(C(=O)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 14, 14, 33, 33, 33, 154, 154, 154, 183, 201, 201, 201, 201, 201, 154, 154, 33, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 14, 33, 33, 33, 33, 154, 183, 183, 201, 201, 33, 33, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 51, 34, 50, 35, 36, 27, 5, 37, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 512 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113320 none CC1CCCN(C(=O)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 154, 101, 154, 101, 101, 35, 35, 35, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 35, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 101, 35, 35, 35, 35, 7, 4, 4, 2, 2, 35, 35, 201, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 550 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113320 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113320/1 /scratch/stefan/7770410/working/building/REAL300020113320 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 238) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/238 `/scratch/stefan/7770410/working/3D/238' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCN(C(=O)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1) `REAL300020113320.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113320 none CC1CCCN(C(=O)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 34, 34, 18, 6, 19, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 26, 34, 34, 34, 34, 34, 13, 13, 1, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 6, 1, 1, 1, 1, 13, 26, 26, 34, 34, 1, 1, 34, 34] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50, 51]) total number of confs: 204 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113320 none CC1CCCN(C(=O)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [154, 154, 154, 154, 154, 102, 56, 102, 56, 56, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 13, 154, 154, 154, 154, 154, 154, 154, 154, 154, 154, 154, 56, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 154, 154] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 428 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113320 none CC1CCCN(C(=O)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 34, 34, 34, 154, 154, 154, 183, 201, 201, 201, 201, 201, 154, 154, 34, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 15, 34, 34, 34, 34, 154, 183, 183, 201, 201, 34, 34, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 51, 34, 50, 35, 36, 27, 5, 37, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 513 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113320 none CC1CCCN(C(=O)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 154, 101, 154, 101, 101, 35, 35, 35, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 35, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 101, 35, 35, 35, 35, 7, 4, 4, 2, 2, 35, 35, 201, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 550 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113320 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113320 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113320/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113320/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113320 Building REAL300020113321 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113321' /scratch/stefan/7770410/working/building/REAL300020113321 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113321 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113321/0 /scratch/stefan/7770410/working/building/REAL300020113321 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/239 `/scratch/stefan/7770410/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NC(C)=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113321.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113321 none COC1=NC(C)=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 47, 64, 79, 79, 79, 79, 11, 11, 1, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 11, 47, 47, 64, 64, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 313 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113321 none COC1=NC(C)=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 96, 96, 96, 96, 96, 39, 39, 39, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 11, 96, 96, 96, 96, 96, 96, 96, 96, 39, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 231 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113321 none COC1=NC(C)=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 96, 96, 96, 166, 201, 201, 201, 201, 201, 96, 96, 20, 2, 2, 2, 2, 2, 2, 1, 1, 6, 20, 20, 20, 20, 96, 166, 166, 201, 201, 20, 20] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 735 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113321 none COC1=NC(C)=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 158, 158, 158, 80, 80, 80, 17, 17, 17, 7, 4, 1, 1, 1, 1, 1, 1, 17, 17, 80, 201, 201, 201, 201, 201, 201, 201, 201, 158, 80, 80, 80, 80, 17, 7, 7, 4, 4, 80, 80] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 538 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113321 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113321/1 /scratch/stefan/7770410/working/building/REAL300020113321 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 240) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/240 `/scratch/stefan/7770410/working/3D/240' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NC(C)=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113321.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113321 none COC1=NC(C)=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 47, 64, 79, 79, 79, 79, 11, 11, 1, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 11, 47, 47, 64, 64, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 313 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113321 none COC1=NC(C)=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 100, 100, 100, 100, 100, 40, 40, 40, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 11, 100, 100, 100, 100, 100, 100, 100, 100, 40, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 237 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113321 none COC1=NC(C)=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 100, 100, 100, 168, 201, 201, 201, 201, 201, 100, 100, 20, 2, 2, 2, 2, 2, 2, 1, 1, 6, 20, 20, 20, 20, 100, 168, 168, 201, 201, 20, 20] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 718 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113321 none COC1=NC(C)=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 158, 158, 158, 81, 81, 81, 17, 17, 17, 7, 4, 1, 1, 1, 1, 1, 1, 17, 17, 81, 201, 201, 201, 201, 201, 201, 201, 201, 158, 81, 81, 81, 81, 17, 7, 7, 4, 4, 81, 81] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 538 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113321 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113321 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113321/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113321/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113321 Building REAL300020113322 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113322' /scratch/stefan/7770410/working/building/REAL300020113322 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113322 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113322/0 /scratch/stefan/7770410/working/building/REAL300020113322 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/241 `/scratch/stefan/7770410/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=COC(C2CC2)=N1) `REAL300020113322.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113322 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=COC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 12, 12, 12, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 12, 48, 48, 48, 48, 48, 135, 135, 48, 48, 12, 12, 12, 12, 1, 6, 6, 8, 8, 12, 12, 48, 135, 135, 135, 135, 135] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 401 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113322 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=COC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 37, 37, 37, 135, 135, 135, 184, 201, 201, 201, 201, 201, 135, 135, 37, 13, 13, 13, 1, 1, 1, 1, 13, 13, 37, 37, 37, 37, 135, 184, 184, 201, 201, 37, 37, 13, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 584 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113322 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=COC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [155, 155, 55, 55, 55, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 55, 155, 155, 155, 155, 155, 201, 201, 155, 155, 55, 55, 55, 55, 8, 4, 4, 2, 2, 55, 55, 155, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 593 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113322 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=COC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 40, 56, 56, 56, 56, 56, 12, 12, 1, 6, 6, 6, 6, 6, 37, 37, 6, 6, 1, 1, 1, 1, 12, 40, 40, 56, 56, 1, 1, 6, 37, 37, 37, 37, 37] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 307 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113322 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=COC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 6, 6, 6, 48, 48, 48, 115, 155, 155, 155, 155, 155, 48, 48, 6, 1, 1, 1, 1, 1, 13, 13, 1, 2, 6, 6, 6, 6, 48, 115, 115, 155, 155, 6, 6, 1, 13, 13, 13, 13, 13] 201 rigid atoms, others: [1, 39, 19, 20, 21, 22, 23, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 628 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113322 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113322/1 /scratch/stefan/7770410/working/building/REAL300020113322 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 242) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/242 `/scratch/stefan/7770410/working/3D/242' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=COC(C2CC2)=N1) `REAL300020113322.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113322 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=COC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 12, 12, 12, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 12, 48, 48, 48, 48, 48, 136, 136, 48, 48, 12, 12, 12, 12, 1, 6, 6, 8, 8, 12, 12, 48, 136, 136, 136, 136, 136] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 405 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113322 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=COC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 36, 36, 36, 136, 136, 136, 184, 201, 201, 201, 201, 201, 136, 136, 36, 13, 13, 13, 1, 1, 1, 1, 13, 13, 36, 36, 36, 36, 136, 184, 184, 201, 201, 36, 36, 13, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 576 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113322 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=COC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 55, 55, 55, 10, 10, 10, 4, 2, 1, 1, 1, 1, 1, 1, 10, 10, 55, 158, 158, 158, 158, 158, 201, 201, 158, 158, 55, 55, 55, 55, 10, 4, 4, 2, 2, 55, 55, 158, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 594 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113322 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=COC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 38, 54, 54, 54, 54, 54, 12, 12, 1, 6, 6, 6, 6, 6, 36, 36, 6, 6, 1, 1, 1, 1, 12, 38, 38, 54, 54, 1, 1, 6, 36, 36, 36, 36, 36] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 299 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113322 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=COC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 6, 6, 6, 48, 48, 48, 115, 155, 155, 155, 155, 155, 48, 48, 6, 1, 1, 1, 1, 1, 13, 13, 1, 2, 6, 6, 6, 6, 48, 115, 115, 155, 155, 6, 6, 1, 13, 13, 13, 13, 13] 201 rigid atoms, others: [1, 39, 19, 20, 21, 22, 23, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 628 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113322 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113322 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113322/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113322/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113322 Building REAL300020113323 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113323' /scratch/stefan/7770410/working/building/REAL300020113323 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113323 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113323/0 /scratch/stefan/7770410/working/building/REAL300020113323 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/243 `/scratch/stefan/7770410/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@H]1C[C@@H]1C1=CC=CC=C1) `REAL300020113323.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113323 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@H]1C[C@@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 10, 10, 10, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 10, 37, 123, 123, 123, 123, 123, 128, 128, 123, 128, 128, 37, 10, 10, 10, 10, 1, 5, 5, 7, 7, 10, 10, 123, 123, 128, 128, 123, 128, 128] 201 rigid atoms, others: [35, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 379 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113323 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@H]1C[C@@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 3, 17, 17, 43, 43, 43, 128, 128, 128, 182, 201, 201, 201, 201, 201, 128, 128, 43, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 17, 43, 43, 43, 43, 128, 182, 182, 201, 201, 43, 43, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 48, 22, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 604 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113323 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@H]1C[C@@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 43, 43, 43, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 43, 104, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 104, 43, 43, 43, 43, 7, 4, 4, 2, 2, 43, 43, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 596 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113323 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@H]1C[C@@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 30, 43, 43, 43, 43, 43, 10, 10, 1, 6, 34, 34, 34, 34, 34, 43, 43, 34, 43, 43, 6, 1, 1, 1, 1, 10, 30, 30, 43, 43, 1, 1, 34, 34, 43, 43, 34, 43, 43] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 40, 41, 34, 18, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 299 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113323 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@H]1C[C@@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 34, 34, 34, 123, 123, 123, 179, 201, 201, 201, 201, 201, 123, 123, 34, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 11, 34, 34, 34, 34, 123, 179, 179, 201, 201, 34, 34, 1, 1, 3, 3, 1, 3, 3] 201 rigid atoms, others: [1, 42, 43, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48]) total number of confs: 617 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113323 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113323/1 /scratch/stefan/7770410/working/building/REAL300020113323 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 244) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/244 `/scratch/stefan/7770410/working/3D/244' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@H]1C[C@@H]1C1=CC=CC=C1) `REAL300020113323.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113323 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@H]1C[C@@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 10, 10, 10, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 10, 37, 125, 125, 125, 125, 125, 130, 130, 125, 130, 130, 37, 10, 10, 10, 10, 1, 5, 5, 7, 7, 10, 10, 125, 125, 130, 130, 125, 130, 130] 201 rigid atoms, others: [35, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 383 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113323 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@H]1C[C@@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 3, 17, 17, 46, 46, 46, 130, 130, 130, 182, 201, 201, 201, 201, 201, 130, 130, 46, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 17, 46, 46, 46, 46, 130, 182, 182, 201, 201, 46, 46, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 48, 22, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 607 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113323 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@H]1C[C@@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 42, 42, 42, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 42, 103, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 103, 42, 42, 42, 42, 7, 4, 4, 2, 2, 42, 42, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 594 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113323 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@H]1C[C@@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 29, 42, 42, 42, 42, 42, 10, 10, 1, 6, 34, 34, 34, 34, 34, 46, 46, 34, 46, 46, 6, 1, 1, 1, 1, 10, 29, 29, 42, 42, 1, 1, 34, 34, 46, 46, 34, 46, 46] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 40, 41, 34, 18, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 311 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113323 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@H]1C[C@@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 34, 34, 34, 125, 125, 125, 179, 201, 201, 201, 201, 201, 125, 125, 34, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 11, 34, 34, 34, 34, 125, 179, 179, 201, 201, 34, 34, 1, 1, 3, 3, 1, 3, 3] 201 rigid atoms, others: [1, 42, 43, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48]) total number of confs: 613 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113323 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113323 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113323/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113323/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113323 Building REAL300020113324 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113324' /scratch/stefan/7770410/working/building/REAL300020113324 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113324 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113324/0 /scratch/stefan/7770410/working/building/REAL300020113324 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/245 `/scratch/stefan/7770410/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1CCCN1C(=O)C1CC1) `REAL300020113324.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113324 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1CCCN1C(=O)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 11, 38, 61, 61, 61, 61, 61, 61, 81, 81, 125, 125, 38, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 61, 61, 61, 61, 61, 61, 125, 125, 125, 125, 125] 201 rigid atoms, others: [35, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 457 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113324 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1CCCN1C(=O)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 8, 14, 14, 34, 34, 34, 125, 125, 125, 176, 201, 201, 201, 201, 201, 125, 125, 34, 8, 8, 8, 8, 8, 5, 1, 5, 1, 1, 1, 14, 34, 34, 34, 34, 125, 176, 176, 201, 201, 34, 34, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1] 201 rigid atoms, others: [48, 49, 50, 51, 52, 25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 643 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113324 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1CCCN1C(=O)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 49, 49, 49, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 49, 94, 125, 125, 125, 125, 125, 125, 159, 159, 201, 201, 94, 49, 49, 49, 49, 9, 4, 4, 2, 2, 49, 49, 125, 125, 125, 125, 125, 125, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 683 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113324 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1CCCN1C(=O)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 46, 46, 46, 46, 46, 11, 11, 1, 6, 16, 16, 16, 16, 16, 16, 20, 20, 34, 34, 6, 1, 1, 1, 1, 11, 31, 31, 46, 46, 1, 1, 16, 16, 16, 16, 16, 16, 34, 34, 34, 34, 34] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 40, 41, 34, 18, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 295 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113324 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1CCCN1C(=O)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 16, 16, 16, 61, 61, 61, 101, 123, 123, 123, 123, 123, 61, 61, 16, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 8, 6, 16, 16, 16, 16, 61, 101, 101, 123, 123, 16, 16, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8] 201 rigid atoms, others: [1, 42, 43, 44, 45, 46, 47, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50, 51, 52]) total number of confs: 447 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113324 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113324/1 /scratch/stefan/7770410/working/building/REAL300020113324 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 246) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/246 `/scratch/stefan/7770410/working/3D/246' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1CCCN1C(=O)C1CC1) `REAL300020113324.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113324 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1CCCN1C(=O)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 11, 38, 62, 62, 62, 62, 62, 62, 82, 82, 125, 125, 38, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 62, 62, 62, 62, 62, 62, 125, 125, 125, 125, 125] 201 rigid atoms, others: [35, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 457 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113324 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1CCCN1C(=O)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 8, 14, 14, 34, 34, 34, 125, 125, 125, 176, 201, 201, 201, 201, 201, 125, 125, 34, 8, 8, 8, 8, 8, 5, 1, 5, 1, 1, 1, 14, 34, 34, 34, 34, 125, 176, 176, 201, 201, 34, 34, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1] 201 rigid atoms, others: [48, 49, 50, 51, 52, 25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 644 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113324 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1CCCN1C(=O)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 49, 49, 49, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 49, 94, 125, 125, 125, 125, 125, 125, 159, 159, 201, 201, 94, 49, 49, 49, 49, 9, 4, 4, 2, 2, 49, 49, 125, 125, 125, 125, 125, 125, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 683 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113324 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1CCCN1C(=O)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 46, 46, 46, 46, 46, 11, 11, 1, 6, 16, 16, 16, 16, 16, 16, 20, 20, 34, 34, 6, 1, 1, 1, 1, 11, 31, 31, 46, 46, 1, 1, 16, 16, 16, 16, 16, 16, 34, 34, 34, 34, 34] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 40, 41, 34, 18, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 295 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113324 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1CCCN1C(=O)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 16, 16, 16, 62, 62, 62, 102, 124, 124, 124, 124, 124, 62, 62, 16, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 8, 6, 16, 16, 16, 16, 62, 102, 102, 124, 124, 16, 16, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8] 201 rigid atoms, others: [1, 42, 43, 44, 45, 46, 47, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50, 51, 52]) total number of confs: 449 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113324 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113324 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113324/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113324/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113324 Building REAL300020113325 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113325' /scratch/stefan/7770410/working/building/REAL300020113325 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113325 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113325/0 /scratch/stefan/7770410/working/building/REAL300020113325 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/247 `/scratch/stefan/7770410/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C(C2CC2)NC1=O) `REAL300020113325.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113325 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C(C2CC2)NC1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 43, 51, 51, 51, 51, 106, 106, 51, 51, 51, 43, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 51, 106, 106, 106, 106, 106, 51] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 337 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113325 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C(C2CC2)NC1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 9, 14, 14, 32, 32, 32, 106, 106, 106, 162, 201, 201, 201, 201, 201, 106, 106, 32, 9, 9, 9, 1, 1, 1, 1, 9, 9, 9, 14, 32, 32, 32, 32, 106, 162, 162, 201, 201, 32, 32, 9, 1, 1, 1, 1, 1, 9] 201 rigid atoms, others: [42, 43, 44, 45, 46, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47]) total number of confs: 706 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113325 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C(C2CC2)NC1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [138, 138, 61, 61, 61, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 61, 138, 147, 147, 147, 147, 201, 201, 147, 147, 147, 138, 61, 61, 61, 61, 12, 6, 6, 4, 4, 61, 61, 147, 201, 201, 201, 201, 201, 147] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 613 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113325 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C(C2CC2)NC1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 41, 57, 62, 62, 62, 62, 11, 11, 1, 6, 10, 10, 10, 10, 32, 32, 10, 10, 10, 6, 1, 1, 1, 1, 11, 41, 41, 57, 57, 1, 1, 10, 32, 32, 32, 32, 32, 10] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 315 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113325 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C(C2CC2)NC1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 10, 10, 10, 51, 51, 51, 106, 140, 147, 147, 147, 147, 51, 51, 10, 1, 1, 1, 1, 1, 9, 9, 1, 1, 1, 4, 10, 10, 10, 10, 51, 106, 106, 140, 140, 10, 10, 1, 9, 9, 9, 9, 9, 1] 201 rigid atoms, others: [1, 41, 47, 19, 20, 21, 22, 23, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 561 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113325 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113325/1 /scratch/stefan/7770410/working/building/REAL300020113325 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 248) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/248 `/scratch/stefan/7770410/working/3D/248' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C(C2CC2)NC1=O) `REAL300020113325.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113325 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C(C2CC2)NC1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 43, 51, 51, 51, 51, 107, 107, 51, 51, 51, 43, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 51, 107, 107, 107, 107, 107, 51] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 339 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113325 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C(C2CC2)NC1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 9, 14, 14, 33, 33, 33, 107, 107, 107, 162, 201, 201, 201, 201, 201, 107, 107, 33, 9, 9, 9, 1, 1, 1, 1, 9, 9, 9, 14, 33, 33, 33, 33, 107, 162, 162, 201, 201, 33, 33, 9, 1, 1, 1, 1, 1, 9] 201 rigid atoms, others: [42, 43, 44, 45, 46, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47]) total number of confs: 705 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113325 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C(C2CC2)NC1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [138, 138, 61, 61, 61, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 61, 138, 147, 147, 147, 147, 201, 201, 147, 147, 147, 138, 61, 61, 61, 61, 12, 6, 6, 4, 4, 61, 61, 147, 201, 201, 201, 201, 201, 147] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 611 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113325 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C(C2CC2)NC1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 40, 56, 61, 61, 61, 61, 11, 11, 1, 6, 10, 10, 10, 10, 33, 33, 10, 10, 10, 6, 1, 1, 1, 1, 11, 40, 40, 56, 56, 1, 1, 10, 33, 33, 33, 33, 33, 10] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 314 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113325 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C(C2CC2)NC1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 10, 10, 10, 51, 51, 51, 106, 140, 147, 147, 147, 147, 51, 51, 10, 1, 1, 1, 1, 1, 9, 9, 1, 1, 1, 4, 10, 10, 10, 10, 51, 106, 106, 140, 140, 10, 10, 1, 9, 9, 9, 9, 9, 1] 201 rigid atoms, others: [1, 41, 47, 19, 20, 21, 22, 23, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 561 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113325 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113325 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113325/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113325/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113325 Building REAL300020113326 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113326' /scratch/stefan/7770410/working/building/REAL300020113326 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113326 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113326/0 /scratch/stefan/7770410/working/building/REAL300020113326 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/249 `/scratch/stefan/7770410/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1C2CC3=CC=CC=C3C21) `REAL300020113326.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113326 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1C2CC3=CC=CC=C3C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 10, 25, 98, 98, 98, 98, 98, 98, 98, 98, 98, 25, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 98, 98, 98, 98, 98, 98, 98, 98, 98] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 277 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113326 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1C2CC3=CC=CC=C3C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 44, 44, 44, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 44, 79, 201, 201, 201, 201, 201, 201, 201, 201, 201, 79, 44, 44, 44, 44, 9, 5, 5, 3, 3, 44, 44, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 586 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113326 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1C2CC3=CC=CC=C3C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 28, 42, 44, 44, 44, 44, 10, 10, 1, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 10, 28, 28, 42, 42, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113326 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1C2CC3=CC=CC=C3C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 24, 24, 24, 98, 98, 98, 157, 201, 201, 201, 201, 201, 98, 98, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 24, 24, 24, 24, 98, 157, 157, 201, 201, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 732 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113326 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113326/1 /scratch/stefan/7770410/working/building/REAL300020113326 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 250) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/250 `/scratch/stefan/7770410/working/3D/250' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1C2CC3=CC=CC=C3C21) `REAL300020113326.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113326/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113326 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1C2CC3=CC=CC=C3C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 10, 25, 98, 98, 98, 98, 98, 98, 98, 98, 98, 25, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 98, 98, 98, 98, 98, 98, 98, 98, 98] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 277 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113326 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1C2CC3=CC=CC=C3C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 44, 44, 44, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 44, 79, 201, 201, 201, 201, 201, 201, 201, 201, 201, 79, 44, 44, 44, 44, 9, 5, 5, 3, 3, 44, 44, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 586 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113326 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1C2CC3=CC=CC=C3C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 28, 42, 44, 44, 44, 44, 10, 10, 1, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 10, 28, 28, 42, 42, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113326 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1C2CC3=CC=CC=C3C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 24, 24, 24, 98, 98, 98, 157, 201, 201, 201, 201, 201, 98, 98, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 24, 24, 24, 24, 98, 157, 157, 201, 201, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 732 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113326 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113326 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113326/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113326/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113326 Building REAL300020113327 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113327' /scratch/stefan/7770410/working/building/REAL300020113327 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113327 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113327/0 /scratch/stefan/7770410/working/building/REAL300020113327 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/251 `/scratch/stefan/7770410/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NO1) `REAL300020113327.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113327 none COCC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 22, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 30, 44, 44, 44, 44, 44, 10, 10, 1, 6, 6, 28, 28, 28, 22, 22, 6, 6, 1, 1, 1, 1, 10, 30, 30, 44, 44, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 269 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113327 none COCC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 99, 38, 38, 38, 38, 38, 38, 10, 10, 10, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 10, 38, 38, 127, 127, 127, 99, 99, 38, 38, 10, 10, 10, 10, 1, 5, 5, 7, 7, 10, 10] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 466 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113327 none COCC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 38, 38, 38, 89, 119, 119, 119, 119, 119, 38, 38, 6, 1, 1, 9, 9, 9, 5, 5, 1, 1, 6, 6, 6, 6, 38, 89, 89, 119, 119, 6, 6] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 25, 26] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 489 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113327 none COCC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 120, 120, 120, 120, 120, 120, 44, 44, 44, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 44, 120, 120, 201, 201, 201, 201, 201, 120, 120, 44, 44, 44, 44, 7, 4, 4, 2, 2, 44, 44] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 789 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113327 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113327/1 /scratch/stefan/7770410/working/building/REAL300020113327 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 252) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/252 `/scratch/stefan/7770410/working/3D/252' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NO1) `REAL300020113327.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113327/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113327 none COCC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 23, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 30, 45, 45, 45, 45, 45, 10, 10, 1, 6, 6, 29, 29, 29, 23, 23, 6, 6, 1, 1, 1, 1, 10, 30, 30, 45, 45, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 278 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113327 none COCC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 98, 38, 38, 38, 38, 38, 38, 10, 10, 10, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 10, 38, 38, 127, 127, 127, 98, 98, 38, 38, 10, 10, 10, 10, 1, 5, 5, 7, 7, 10, 10] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 465 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113327 none COCC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 38, 38, 38, 88, 119, 119, 119, 119, 119, 38, 38, 6, 1, 1, 9, 9, 9, 5, 5, 1, 1, 6, 6, 6, 6, 38, 88, 88, 119, 119, 6, 6] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 25, 26] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 492 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113327 none COCC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 118, 118, 118, 118, 118, 118, 44, 44, 44, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 44, 118, 118, 201, 201, 201, 201, 201, 118, 118, 44, 44, 44, 44, 7, 4, 4, 2, 2, 44, 44] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 794 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113327 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113327 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113327/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113327/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113327 Building REAL300020113328 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113328' /scratch/stefan/7770410/working/building/REAL300020113328 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113328 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113328/0 /scratch/stefan/7770410/working/building/REAL300020113328 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/253 `/scratch/stefan/7770410/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=NC(C2CC2)=NO1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113328.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113328 none O=C(CCC1=NC(C2CC2)=NO1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 5, 5, 5, 8, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 27, 22, 10, 10, 10, 1, 1, 1, 1, 10, 10, 39, 39, 59, 59, 59, 126, 126, 126, 174, 201, 201, 201, 201, 201, 126, 126, 59, 27, 27, 22, 22, 1, 1, 1, 1, 1, 39, 59, 59, 59, 59, 126, 174, 174, 201, 201, 59, 59] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 736 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113328 none O=C(CCC1=NC(C2CC2)=NO1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 5, 5, 5, 8, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 145, 145, 153, 153, 153, 201, 201, 153, 153, 36, 36, 36, 8, 8, 8, 5, 3, 1, 1, 1, 1, 1, 1, 8, 8, 36, 145, 145, 145, 145, 201, 201, 201, 201, 201, 64, 36, 36, 36, 36, 8, 5, 5, 3, 3, 36, 36] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 764 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113328 none O=C(CCC1=NC(C2CC2)=NO1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 5, 5, 5, 8, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 18, 18, 26, 26, 26, 59, 59, 26, 26, 1, 1, 1, 1, 1, 8, 8, 8, 22, 34, 35, 35, 35, 35, 8, 8, 1, 18, 18, 18, 18, 59, 59, 59, 59, 59, 5, 1, 1, 1, 1, 8, 22, 22, 34, 34, 1, 1] 201 rigid atoms, others: [48, 39, 40, 41, 42, 12, 13, 14, 15, 16, 49, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 308 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113328 none O=C(CCC1=NC(C2CC2)=NO1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 5, 5, 5, 8, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 10, 6, 1, 1, 1, 1, 1, 10, 10, 1, 1, 14, 14, 26, 26, 26, 64, 64, 64, 112, 145, 146, 146, 146, 146, 64, 64, 26, 10, 10, 6, 6, 10, 10, 10, 10, 10, 14, 26, 26, 26, 26, 64, 112, 112, 145, 145, 26, 26] 201 rigid atoms, others: [3, 4, 5, 6, 7, 10, 11] set([0, 1, 2, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 596 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113328 none O=C(CCC1=NC(C2CC2)=NO1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 5, 5, 5, 8, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 56, 56, 64, 64, 64, 126, 126, 64, 64, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 8, 8, 8, 8, 1, 1, 8, 56, 56, 56, 56, 126, 126, 126, 126, 126, 21, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [43, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 442 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113328 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113328/1 /scratch/stefan/7770410/working/building/REAL300020113328 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 254) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/254 `/scratch/stefan/7770410/working/3D/254' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=NC(C2CC2)=NO1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113328.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113328/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113328 none O=C(CCC1=NC(C2CC2)=NO1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 5, 5, 5, 8, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 26, 22, 10, 10, 10, 1, 1, 1, 1, 10, 10, 38, 38, 59, 59, 59, 126, 126, 126, 173, 201, 201, 201, 201, 201, 126, 126, 59, 26, 26, 22, 22, 1, 1, 1, 1, 1, 38, 59, 59, 59, 59, 126, 173, 173, 201, 201, 59, 59] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 734 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113328 none O=C(CCC1=NC(C2CC2)=NO1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 5, 5, 5, 8, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 145, 145, 153, 153, 153, 201, 201, 153, 153, 36, 36, 36, 8, 8, 8, 5, 3, 1, 1, 1, 1, 1, 1, 8, 8, 36, 145, 145, 145, 145, 201, 201, 201, 201, 201, 63, 36, 36, 36, 36, 8, 5, 5, 3, 3, 36, 36] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 768 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113328 none O=C(CCC1=NC(C2CC2)=NO1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 5, 5, 5, 8, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 18, 18, 25, 25, 25, 59, 59, 25, 25, 1, 1, 1, 1, 1, 8, 8, 8, 22, 34, 35, 35, 35, 35, 8, 8, 1, 18, 18, 18, 18, 59, 59, 59, 59, 59, 5, 1, 1, 1, 1, 8, 22, 22, 34, 34, 1, 1] 201 rigid atoms, others: [48, 39, 40, 41, 42, 12, 13, 14, 15, 16, 49, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 311 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113328 none O=C(CCC1=NC(C2CC2)=NO1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 5, 5, 5, 8, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 10, 6, 1, 1, 1, 1, 1, 10, 10, 1, 1, 14, 14, 25, 25, 25, 64, 64, 64, 111, 145, 146, 146, 146, 146, 64, 64, 25, 10, 10, 6, 6, 10, 10, 10, 10, 10, 14, 25, 25, 25, 25, 64, 111, 111, 145, 145, 25, 25] 201 rigid atoms, others: [3, 4, 5, 6, 7, 10, 11] set([0, 1, 2, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 594 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113328 none O=C(CCC1=NC(C2CC2)=NO1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 5, 5, 5, 8, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 57, 57, 64, 64, 64, 126, 126, 64, 64, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 8, 8, 8, 8, 1, 1, 8, 57, 57, 57, 57, 126, 126, 126, 126, 126, 21, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [43, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 447 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113328 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113328 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113328/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113328/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113328 Building REAL300020113329 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113329' /scratch/stefan/7770410/working/building/REAL300020113329 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113329 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113329/0 /scratch/stefan/7770410/working/building/REAL300020113329 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/255 `/scratch/stefan/7770410/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C)=C1CC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113329.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113329 none CC1=NOC(C)=C1CC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 39, 39, 26, 17, 6, 17, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 26, 40, 42, 42, 42, 42, 9, 9, 1, 39, 39, 39, 39, 39, 39, 26, 26, 17, 17, 17, 17, 6, 1, 1, 1, 1, 9, 26, 26, 40, 40, 1, 1] 201 rigid atoms, others: [45, 44, 42, 43, 12, 13, 14, 15, 16, 51, 52, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50]) total number of confs: 307 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113329 none CC1=NOC(C)=C1CC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 118, 118, 118, 83, 71, 30, 71, 30, 30, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 118, 118, 118, 118, 118, 118, 83, 83, 71, 71, 71, 71, 30, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [46, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 425 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113329 none CC1=NOC(C)=C1CC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 11, 11, 22, 22, 22, 39, 39, 39, 118, 118, 118, 167, 201, 201, 201, 201, 201, 118, 118, 39, 2, 2, 2, 2, 2, 2, 6, 6, 11, 11, 11, 11, 22, 39, 39, 39, 39, 118, 167, 167, 201, 201, 39, 39] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 725 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113329 none CC1=NOC(C)=C1CC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 150, 145, 93, 145, 93, 93, 43, 43, 43, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 43, 201, 201, 201, 201, 201, 201, 150, 150, 145, 145, 145, 145, 93, 43, 43, 43, 43, 10, 5, 5, 3, 3, 43, 43] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 638 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113329 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113329/1 /scratch/stefan/7770410/working/building/REAL300020113329 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 256) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/256 `/scratch/stefan/7770410/working/3D/256' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C)=C1CC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113329.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113329 none CC1=NOC(C)=C1CC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 39, 39, 26, 17, 6, 17, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 26, 40, 42, 42, 42, 42, 9, 9, 1, 39, 39, 39, 39, 39, 39, 26, 26, 17, 17, 17, 17, 6, 1, 1, 1, 1, 9, 26, 26, 40, 40, 1, 1] 201 rigid atoms, others: [45, 44, 42, 43, 12, 13, 14, 15, 16, 51, 52, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50]) total number of confs: 307 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113329 none CC1=NOC(C)=C1CC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 118, 118, 118, 83, 71, 30, 71, 30, 30, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 118, 118, 118, 118, 118, 118, 83, 83, 71, 71, 71, 71, 30, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [46, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 425 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113329 none CC1=NOC(C)=C1CC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 11, 11, 22, 22, 22, 39, 39, 39, 118, 118, 118, 167, 201, 201, 201, 201, 201, 118, 118, 39, 2, 2, 2, 2, 2, 2, 6, 6, 11, 11, 11, 11, 22, 39, 39, 39, 39, 118, 167, 167, 201, 201, 39, 39] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 725 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113329 none CC1=NOC(C)=C1CC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 150, 145, 94, 145, 94, 94, 43, 43, 43, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 43, 201, 201, 201, 201, 201, 201, 150, 150, 145, 145, 145, 145, 94, 43, 43, 43, 43, 10, 5, 5, 3, 3, 43, 43] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 634 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113329 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113329 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113329/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113329/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113329 Building REAL300020113330 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113330' /scratch/stefan/7770410/working/building/REAL300020113330 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113330 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113330/0 /scratch/stefan/7770410/working/building/REAL300020113330 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/257 `/scratch/stefan/7770410/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2C=CC=NN21) `REAL300020113330.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113330 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2C=CC=NN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 9, 12, 18, 18, 18, 18, 1, 1, 13, 53, 95, 95, 95, 95, 95, 95, 95, 95, 53, 13, 13, 13, 13, 1, 9, 9, 12, 12, 13, 13, 95, 95, 95, 95, 95] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 254 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113330 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2C=CC=NN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 107, 107, 107, 21, 21, 21, 6, 4, 1, 1, 1, 1, 1, 1, 21, 21, 107, 189, 201, 201, 201, 201, 201, 201, 201, 201, 189, 107, 107, 107, 107, 21, 6, 6, 4, 4, 107, 107, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 537 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113330 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2C=CC=NN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 64, 83, 106, 106, 106, 106, 13, 13, 1, 6, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 13, 64, 64, 83, 83, 1, 1, 21, 21, 21, 21, 21] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 392 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113330 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2C=CC=NN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 21, 21, 21, 95, 95, 95, 174, 201, 201, 201, 201, 201, 95, 95, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 21, 95, 174, 174, 201, 201, 21, 21, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 699 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113330 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113330/1 /scratch/stefan/7770410/working/building/REAL300020113330 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 258) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/258 `/scratch/stefan/7770410/working/3D/258' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2C=CC=NN21) `REAL300020113330.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113330 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2C=CC=NN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 12, 12, 12, 1, 1, 1, 1, 1, 9, 12, 18, 18, 18, 18, 1, 1, 12, 52, 97, 97, 97, 97, 97, 97, 97, 97, 52, 12, 12, 12, 12, 1, 9, 9, 12, 12, 12, 12, 97, 97, 97, 97, 97] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 257 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113330 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2C=CC=NN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [190, 190, 107, 107, 107, 23, 23, 23, 6, 4, 1, 1, 1, 1, 1, 1, 23, 23, 107, 190, 201, 201, 201, 201, 201, 201, 201, 201, 190, 107, 107, 107, 107, 23, 6, 6, 4, 4, 107, 107, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 533 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113330 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2C=CC=NN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 63, 82, 104, 104, 104, 104, 12, 12, 1, 6, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 12, 63, 63, 82, 82, 1, 1, 21, 21, 21, 21, 21] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 389 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113330 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2C=CC=NN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 21, 21, 21, 97, 97, 97, 174, 201, 201, 201, 201, 201, 97, 97, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 21, 97, 174, 174, 201, 201, 21, 21, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 690 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113330 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113330 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113330/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113330/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113330 Building REAL300020113331 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113331' /scratch/stefan/7770410/working/building/REAL300020113331 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113331 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113331/0 /scratch/stefan/7770410/working/building/REAL300020113331 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/259 `/scratch/stefan/7770410/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2NC=CC(=O)N2N=C1) `REAL300020113331.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113331 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2NC=CC(=O)N2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 11, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 5, 5, 5, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 5, 20, 29, 29, 29, 29, 29, 29, 29, 29, 29, 20, 5, 5, 5, 5, 1, 5, 5, 7, 7, 5, 5, 29, 29, 29, 29] 40 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 92 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113331 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2NC=CC(=O)N2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 11, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 17, 17, 17, 8, 8, 8, 5, 2, 1, 1, 1, 1, 1, 1, 8, 8, 17, 34, 40, 40, 40, 40, 40, 40, 40, 40, 40, 34, 17, 17, 17, 17, 8, 5, 5, 2, 2, 17, 17, 40, 40, 40, 40] 40 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 113 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113331 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2NC=CC(=O)N2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 11, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 11, 16, 16, 16, 16, 16, 5, 5, 1, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 5, 11, 11, 16, 16, 1, 1, 20, 20, 20, 20] 40 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113331 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2NC=CC(=O)N2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 11, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 20, 20, 20, 29, 29, 29, 36, 40, 40, 40, 40, 40, 29, 29, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 20, 20, 20, 20, 29, 36, 36, 40, 40, 20, 20, 1, 1, 1, 1] 40 rigid atoms, others: [1, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 129 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113331 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113331/1 /scratch/stefan/7770410/working/building/REAL300020113331 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 260) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/260 `/scratch/stefan/7770410/working/3D/260' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2NC=CC(=O)N2N=C1) `REAL300020113331.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113331 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2NC=CC(=O)N2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 11, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 5, 5, 5, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 5, 20, 29, 29, 29, 29, 29, 29, 29, 29, 29, 20, 5, 5, 5, 5, 1, 5, 5, 7, 7, 5, 5, 29, 29, 29, 29] 40 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 92 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113331 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2NC=CC(=O)N2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 11, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 17, 17, 17, 8, 8, 8, 5, 2, 1, 1, 1, 1, 1, 1, 8, 8, 17, 34, 40, 40, 40, 40, 40, 40, 40, 40, 40, 34, 17, 17, 17, 17, 8, 5, 5, 2, 2, 17, 17, 40, 40, 40, 40] 40 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 113 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113331 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2NC=CC(=O)N2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 11, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 11, 16, 16, 16, 16, 16, 5, 5, 1, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 5, 11, 11, 16, 16, 1, 1, 20, 20, 20, 20] 40 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113331 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2NC=CC(=O)N2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 11, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 20, 20, 20, 29, 29, 29, 36, 40, 40, 40, 40, 40, 29, 29, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 20, 20, 20, 20, 29, 36, 36, 40, 40, 20, 20, 1, 1, 1, 1] 40 rigid atoms, others: [1, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 129 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113331 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113331 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113331/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113331/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113331 Building REAL300020113332 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113332' /scratch/stefan/7770410/working/building/REAL300020113332 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113332 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113332/0 /scratch/stefan/7770410/working/building/REAL300020113332 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/261 `/scratch/stefan/7770410/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2C=CC=NN12) `REAL300020113332.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113332 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2C=CC=NN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 18, 18, 18, 18, 1, 1, 13, 54, 88, 88, 88, 88, 88, 88, 88, 88, 54, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 88, 88, 88, 88] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 248 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113332 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2C=CC=NN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [187, 187, 101, 101, 101, 21, 21, 21, 6, 4, 1, 1, 1, 1, 1, 1, 21, 21, 101, 187, 201, 201, 201, 201, 201, 201, 201, 201, 187, 101, 101, 101, 101, 21, 6, 6, 4, 4, 101, 101, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 541 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113332 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2C=CC=NN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 61, 79, 99, 99, 99, 99, 13, 13, 1, 6, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 13, 61, 61, 79, 79, 1, 1, 15, 15, 15, 15] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 364 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113332 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2C=CC=NN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 15, 15, 15, 88, 88, 88, 167, 201, 201, 201, 201, 201, 88, 88, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 15, 15, 15, 15, 88, 167, 167, 201, 201, 15, 15, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 718 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113332 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113332/1 /scratch/stefan/7770410/working/building/REAL300020113332 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 262) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/262 `/scratch/stefan/7770410/working/3D/262' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2C=CC=NN12) `REAL300020113332.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113332/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113332 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2C=CC=NN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 18, 18, 18, 18, 1, 1, 13, 54, 88, 88, 88, 88, 88, 88, 88, 88, 54, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 88, 88, 88, 88] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 248 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113332 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2C=CC=NN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [186, 186, 100, 100, 100, 21, 21, 21, 6, 4, 1, 1, 1, 1, 1, 1, 21, 21, 100, 186, 201, 201, 201, 201, 201, 201, 201, 201, 186, 100, 100, 100, 100, 21, 6, 6, 4, 4, 100, 100, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 541 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113332 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2C=CC=NN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 61, 79, 99, 99, 99, 99, 13, 13, 1, 6, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 13, 61, 61, 79, 79, 1, 1, 15, 15, 15, 15] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 364 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113332 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2C=CC=NN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 15, 15, 15, 88, 88, 88, 167, 201, 201, 201, 201, 201, 88, 88, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 15, 15, 15, 15, 88, 167, 167, 201, 201, 15, 15, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 718 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113332 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113332 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113332/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113332/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113332 Building REAL300020113333 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113333' /scratch/stefan/7770410/working/building/REAL300020113333 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113333 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113333/0 /scratch/stefan/7770410/working/building/REAL300020113333 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/263 `/scratch/stefan/7770410/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113333.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113333 none CN(C)C(=O)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [130, 129, 130, 75, 129, 25, 25, 25, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 130, 130, 130, 130, 130, 130, 75, 75, 25, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 482 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113333 none CN(C)C(=O)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 160, 201, 75, 75, 75, 37, 37, 37, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 37, 201, 201, 201, 201, 201, 201, 160, 160, 75, 37, 37, 37, 37, 8, 4, 4, 2, 2, 37, 37] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 762 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113333 none CN(C)C(=O)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 42, 43, 24, 42, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 25, 37, 37, 37, 37, 37, 8, 8, 1, 43, 43, 43, 43, 43, 43, 24, 24, 6, 1, 1, 1, 1, 8, 25, 25, 37, 37, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 287 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113333 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113333/1 /scratch/stefan/7770410/working/building/REAL300020113333 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 264) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/264 `/scratch/stefan/7770410/working/3D/264' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113333.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113333 none CN(C)C(=O)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [130, 129, 130, 75, 129, 25, 25, 25, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 130, 130, 130, 130, 130, 130, 75, 75, 25, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 482 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113333 none CN(C)C(=O)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 160, 201, 75, 75, 75, 37, 37, 37, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 37, 201, 201, 201, 201, 201, 201, 160, 160, 75, 37, 37, 37, 37, 8, 4, 4, 2, 2, 37, 37] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 762 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113333 none CN(C)C(=O)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 42, 43, 24, 42, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 25, 37, 37, 37, 37, 37, 8, 8, 1, 43, 43, 43, 43, 43, 43, 24, 24, 6, 1, 1, 1, 1, 8, 25, 25, 37, 37, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 287 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113333 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113333 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113333/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113333/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113333 Building REAL300020113334 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113334' /scratch/stefan/7770410/working/building/REAL300020113334 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113334 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113334/0 /scratch/stefan/7770410/working/building/REAL300020113334 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/265 `/scratch/stefan/7770410/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=C(Cl)S1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113334.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113334 none O=C(CC1=CC=C(Cl)S1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 16, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 26, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 8, 8, 8, 26, 38, 39, 39, 39, 39, 8, 8, 1, 26, 26, 47, 47, 5, 1, 1, 1, 1, 8, 26, 26, 38, 38, 1, 1] 201 rigid atoms, others: [32, 33, 34, 40, 9, 10, 11, 12, 13, 41, 25, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) total number of confs: 279 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113334 none O=C(CC1=CC=C(Cl)S1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 16, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 95, 133, 133, 133, 133, 133, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 95, 95, 133, 133, 22, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [35, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 433 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113334 none O=C(CC1=CC=C(Cl)S1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 16, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 4, 1, 1, 1, 1, 1, 1, 1, 26, 26, 47, 47, 47, 133, 133, 133, 182, 201, 201, 201, 201, 201, 133, 133, 47, 4, 4, 1, 1, 26, 47, 47, 47, 47, 133, 182, 182, 201, 201, 47, 47] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 28, 29] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 622 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113334 none O=C(CC1=CC=C(Cl)S1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 16, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 187, 201, 201, 201, 201, 201, 39, 39, 39, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 39, 187, 187, 201, 201, 68, 39, 39, 39, 39, 9, 5, 5, 3, 3, 39, 39] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 703 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113334 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113334/1 /scratch/stefan/7770410/working/building/REAL300020113334 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 266) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/266 `/scratch/stefan/7770410/working/3D/266' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=C(Cl)S1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113334.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113334/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113334 none O=C(CC1=CC=C(Cl)S1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 16, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 26, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 8, 8, 8, 26, 38, 39, 39, 39, 39, 8, 8, 1, 26, 26, 47, 47, 5, 1, 1, 1, 1, 8, 26, 26, 38, 38, 1, 1] 201 rigid atoms, others: [32, 33, 34, 40, 9, 10, 11, 12, 13, 41, 25, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) total number of confs: 279 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113334 none O=C(CC1=CC=C(Cl)S1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 16, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 95, 134, 134, 134, 134, 134, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 95, 95, 134, 134, 22, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [35, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 435 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113334 none O=C(CC1=CC=C(Cl)S1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 16, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 4, 1, 1, 1, 1, 1, 1, 1, 26, 26, 47, 47, 47, 134, 134, 134, 182, 201, 201, 201, 201, 201, 134, 134, 47, 4, 4, 1, 1, 26, 47, 47, 47, 47, 134, 182, 182, 201, 201, 47, 47] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 28, 29] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 621 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113334 none O=C(CC1=CC=C(Cl)S1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 16, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 186, 201, 201, 201, 201, 201, 38, 38, 38, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 38, 186, 186, 201, 201, 66, 38, 38, 38, 38, 9, 5, 5, 3, 3, 38, 38] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 702 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113334 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113334 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113334/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113334/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113334 Building REAL300020113335 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113335' /scratch/stefan/7770410/working/building/REAL300020113335 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113335 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113335/0 /scratch/stefan/7770410/working/building/REAL300020113335 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/267 `/scratch/stefan/7770410/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(NS(C)(=O)=O)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113335.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113335 none CC(C)(NS(C)(=O)=O)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 14, 5, 11, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 31, 106, 106, 142, 142, 142, 142, 31, 31, 12, 12, 12, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 12, 106, 106, 106, 106, 106, 106, 142, 142, 142, 142, 31, 12, 12, 12, 12, 1, 5, 5, 7, 7, 12, 12] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 538 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113335 none CC(C)(NS(C)(=O)=O)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 14, 5, 11, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [175, 72, 175, 175, 201, 201, 201, 201, 72, 72, 39, 39, 39, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 39, 175, 175, 175, 175, 175, 175, 201, 201, 201, 201, 72, 39, 39, 39, 39, 7, 4, 4, 2, 2, 39, 39] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 775 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113335 none CC(C)(NS(C)(=O)=O)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 14, 5, 11, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 6, 28, 28, 40, 41, 41, 41, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 29, 41, 41, 41, 41, 41, 12, 12, 1, 28, 28, 28, 28, 28, 28, 40, 41, 41, 41, 6, 1, 1, 1, 1, 12, 29, 29, 41, 41, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 307 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113335 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113335/1 /scratch/stefan/7770410/working/building/REAL300020113335 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 268) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/268 `/scratch/stefan/7770410/working/3D/268' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(NS(C)(=O)=O)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113335.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113335/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113335 none CC(C)(NS(C)(=O)=O)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 14, 5, 11, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 31, 106, 106, 142, 142, 142, 142, 31, 31, 12, 12, 12, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 12, 106, 106, 106, 106, 106, 106, 142, 142, 142, 142, 31, 12, 12, 12, 12, 1, 5, 5, 7, 7, 12, 12] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 538 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113335 none CC(C)(NS(C)(=O)=O)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 14, 5, 11, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [176, 72, 176, 176, 201, 201, 201, 201, 72, 72, 39, 39, 39, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 39, 176, 176, 176, 176, 176, 176, 201, 201, 201, 201, 72, 39, 39, 39, 39, 7, 4, 4, 2, 2, 39, 39] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 774 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113335 none CC(C)(NS(C)(=O)=O)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 14, 5, 11, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 6, 28, 28, 40, 41, 41, 41, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 29, 41, 41, 41, 41, 41, 12, 12, 1, 28, 28, 28, 28, 28, 28, 40, 41, 41, 41, 6, 1, 1, 1, 1, 12, 29, 29, 41, 41, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 307 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113335 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113335 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113335/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113335/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113335 Building REAL300020113336 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113336' /scratch/stefan/7770410/working/building/REAL300020113336 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113336 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113336/0 /scratch/stefan/7770410/working/building/REAL300020113336 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/269 `/scratch/stefan/7770410/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)C1=NOC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020113336.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113336 none CCC(CC)C1=NOC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 13, 8, 13, 17, 8, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 39, 55, 59, 59, 59, 59, 13, 13, 1, 8, 17, 17, 17, 17, 17, 13, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 13, 39, 39, 55, 55, 1, 1, 8] 201 rigid atoms, others: [43, 41, 42, 11, 12, 13, 14, 15, 50, 51, 27, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 52]) total number of confs: 320 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113336 none CCC(CC)C1=NOC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 94, 58, 94, 100, 58, 58, 58, 51, 51, 51, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 58, 100, 100, 100, 100, 100, 94, 100, 100, 100, 100, 100, 51, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 58] 201 rigid atoms, others: [45, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 461 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113336 none CCC(CC)C1=NOC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 1, 3, 5, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 58, 58, 58, 126, 185, 189, 189, 189, 189, 58, 58, 8, 1, 5, 5, 5, 5, 5, 3, 5, 5, 5, 5, 5, 3, 8, 8, 8, 8, 58, 126, 126, 185, 185, 8, 8, 1] 201 rigid atoms, others: [2, 5, 6, 7, 8, 9, 52, 28] set([0, 1, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 786 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113336 none CCC(CC)C1=NOC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 195, 189, 195, 201, 189, 189, 189, 182, 182, 182, 60, 60, 60, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 60, 189, 201, 201, 201, 201, 201, 195, 201, 201, 201, 201, 201, 182, 60, 60, 60, 60, 11, 6, 6, 4, 4, 60, 60, 189] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 601 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113336 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113336/1 /scratch/stefan/7770410/working/building/REAL300020113336 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 270) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/270 `/scratch/stefan/7770410/working/3D/270' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)C1=NOC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020113336.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113336/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113336 none CCC(CC)C1=NOC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 13, 8, 13, 17, 8, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 39, 55, 59, 59, 59, 59, 13, 13, 1, 8, 17, 17, 17, 17, 17, 13, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 13, 39, 39, 55, 55, 1, 1, 8] 201 rigid atoms, others: [43, 41, 42, 11, 12, 13, 14, 15, 50, 51, 27, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 52]) total number of confs: 320 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113336 none CCC(CC)C1=NOC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 94, 58, 94, 100, 58, 58, 58, 51, 51, 51, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 58, 100, 100, 100, 100, 100, 94, 100, 100, 100, 100, 100, 51, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 58] 201 rigid atoms, others: [45, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 461 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113336 none CCC(CC)C1=NOC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 1, 3, 5, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 58, 58, 58, 126, 185, 189, 189, 189, 189, 58, 58, 8, 1, 5, 5, 5, 5, 5, 3, 5, 5, 5, 5, 5, 3, 8, 8, 8, 8, 58, 126, 126, 185, 185, 8, 8, 1] 201 rigid atoms, others: [2, 5, 6, 7, 8, 9, 52, 28] set([0, 1, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 786 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113336 none CCC(CC)C1=NOC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 195, 189, 195, 201, 189, 189, 189, 182, 182, 182, 60, 60, 60, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 60, 189, 201, 201, 201, 201, 201, 195, 201, 201, 201, 201, 201, 182, 60, 60, 60, 60, 11, 6, 6, 4, 4, 60, 60, 189] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 601 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113336 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113336 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113336/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113336/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113336 Building REAL300020113337 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113337' /scratch/stefan/7770410/working/building/REAL300020113337 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113337 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113337/0 /scratch/stefan/7770410/working/building/REAL300020113337 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/271 `/scratch/stefan/7770410/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C1=NOC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020113337.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113337 none CCC(C)C1=NOC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 19, 8, 19, 8, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 34, 50, 55, 55, 55, 55, 13, 13, 1, 8, 22, 22, 22, 22, 22, 19, 19, 19, 19, 6, 1, 1, 1, 1, 13, 34, 34, 50, 50, 1, 1, 8] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49]) total number of confs: 301 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113337 none CCC(C)C1=NOC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 105, 53, 105, 53, 53, 53, 47, 47, 47, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 53, 106, 106, 106, 106, 106, 105, 105, 105, 105, 47, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 53] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 457 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113337 none CCC(C)C1=NOC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 1, 4, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 53, 53, 53, 93, 115, 119, 119, 119, 119, 53, 53, 8, 1, 6, 6, 6, 6, 6, 4, 4, 4, 4, 3, 8, 8, 8, 8, 53, 93, 93, 115, 115, 8, 8, 1] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 49, 27] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 433 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113337 none CCC(C)C1=NOC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 120, 201, 120, 120, 120, 118, 118, 118, 56, 56, 56, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 56, 120, 201, 201, 201, 201, 201, 201, 201, 201, 201, 118, 56, 56, 56, 56, 10, 6, 6, 4, 4, 56, 56, 120] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 825 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113337 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113337/1 /scratch/stefan/7770410/working/building/REAL300020113337 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 272) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/272 `/scratch/stefan/7770410/working/3D/272' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C1=NOC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020113337.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113337/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113337 none CCC(C)C1=NOC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 19, 8, 19, 8, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 35, 51, 56, 56, 56, 56, 13, 13, 1, 8, 22, 22, 22, 22, 22, 19, 19, 19, 19, 6, 1, 1, 1, 1, 13, 35, 35, 51, 51, 1, 1, 8] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49]) total number of confs: 304 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113337 none CCC(C)C1=NOC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 105, 53, 105, 53, 53, 53, 47, 47, 47, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 53, 106, 106, 106, 106, 106, 105, 105, 105, 105, 47, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 53] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 457 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113337 none CCC(C)C1=NOC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 1, 4, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 53, 53, 53, 94, 116, 120, 120, 120, 120, 53, 53, 8, 1, 6, 6, 6, 6, 6, 4, 4, 4, 4, 3, 8, 8, 8, 8, 53, 94, 94, 116, 116, 8, 8, 1] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 49, 27] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 439 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113337 none CCC(C)C1=NOC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 118, 201, 118, 118, 118, 116, 116, 116, 54, 54, 54, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 54, 118, 201, 201, 201, 201, 201, 201, 201, 201, 201, 116, 54, 54, 54, 54, 10, 6, 6, 4, 4, 54, 54, 118] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 831 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113337 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113337 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113337/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113337/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113337 Building REAL300020113338 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113338' /scratch/stefan/7770410/working/building/REAL300020113338 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113338 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113338/0 /scratch/stefan/7770410/working/building/REAL300020113338 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/273 `/scratch/stefan/7770410/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)C2CCC1(C(=O)NC1CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C1)CC2) `REAL300020113338.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113338 none CC1(C)C2CCC1(C(=O)NC1CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 42, 61, 73, 73, 73, 73, 13, 13, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 13, 42, 42, 61, 61, 1, 1, 20, 20, 20, 20] 201 rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 49, 50, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 51, 52, 53, 54]) total number of confs: 300 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113338 none CC1(C)C2CCC1(C(=O)NC1CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 98, 98, 98, 49, 49, 49, 13, 13, 13, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 13, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 49, 13, 13, 13, 13, 1, 7, 7, 9, 9, 13, 13, 98, 98, 98, 98] 201 rigid atoms, others: [12, 44, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 236 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113338 none CC1(C)C2CCC1(C(=O)NC1CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 98, 98, 98, 167, 201, 201, 201, 201, 201, 98, 98, 20, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 6, 20, 20, 20, 20, 98, 167, 167, 201, 201, 20, 20, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 34, 35, 52, 53, 54, 36, 26, 27, 51, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 727 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113338 none CC1(C)C2CCC1(C(=O)NC1CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 142, 142, 142, 74, 74, 74, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 74, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 142, 74, 74, 74, 74, 12, 6, 6, 4, 4, 74, 74, 201, 201, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 503 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113338 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113338/1 /scratch/stefan/7770410/working/building/REAL300020113338 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 274) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/274 `/scratch/stefan/7770410/working/3D/274' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)C2CCC1(C(=O)NC1CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C1)CC2) `REAL300020113338.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113338/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113338 none CC1(C)C2CCC1(C(=O)NC1CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 42, 61, 74, 74, 74, 74, 13, 13, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 13, 42, 42, 61, 61, 1, 1, 20, 20, 20, 20] 201 rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 49, 50, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 51, 52, 53, 54]) total number of confs: 302 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113338 none CC1(C)C2CCC1(C(=O)NC1CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 98, 98, 98, 49, 49, 49, 13, 13, 13, 1, 1, 1, 1, 1, 7, 9, 12, 12, 12, 12, 1, 1, 13, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 49, 13, 13, 13, 13, 1, 7, 7, 9, 9, 13, 13, 98, 98, 98, 98] 201 rigid atoms, others: [12, 44, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 238 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113338 none CC1(C)C2CCC1(C(=O)NC1CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 98, 98, 98, 168, 201, 201, 201, 201, 201, 98, 98, 20, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 6, 20, 20, 20, 20, 98, 168, 168, 201, 201, 20, 20, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 34, 35, 52, 53, 54, 36, 26, 27, 51, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 724 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113338 none CC1(C)C2CCC1(C(=O)NC1CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 143, 143, 143, 75, 75, 75, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 75, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 143, 75, 75, 75, 75, 13, 6, 6, 4, 4, 75, 75, 201, 201, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 503 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113338 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113338 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113338/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113338/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113338 Building REAL300020113339 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113339' /scratch/stefan/7770410/working/building/REAL300020113339 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113339 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113339/0 /scratch/stefan/7770410/working/building/REAL300020113339 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/275 `/scratch/stefan/7770410/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=N1) `REAL300020113339.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113339 none C=CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 53, 16, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 33, 40, 58, 58, 58, 58, 7, 7, 1, 15, 16, 79, 79, 79, 53, 53, 16, 5, 1, 1, 1, 1, 7, 33, 33, 40, 40, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 454 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113339 none C=CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 85, 31, 31, 31, 12, 12, 12, 7, 7, 7, 1, 1, 1, 1, 1, 8, 10, 16, 16, 16, 16, 1, 1, 7, 31, 31, 114, 114, 114, 85, 85, 31, 12, 7, 7, 7, 7, 1, 8, 8, 10, 10, 7, 7] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 456 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113339 none C=CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 1, 1, 1, 1, 1, 7, 7, 7, 16, 16, 16, 31, 31, 31, 91, 101, 121, 121, 121, 121, 31, 31, 16, 1, 1, 16, 16, 16, 7, 7, 1, 7, 16, 16, 16, 16, 31, 91, 91, 101, 101, 16, 16] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 25, 26] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 461 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113339 none C=CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 123, 123, 123, 89, 89, 89, 67, 67, 67, 25, 25, 25, 7, 4, 1, 1, 1, 1, 1, 1, 25, 25, 67, 123, 123, 201, 201, 201, 201, 201, 123, 89, 67, 67, 67, 67, 25, 7, 7, 4, 4, 67, 67] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 728 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113339 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113339/1 /scratch/stefan/7770410/working/building/REAL300020113339 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 276) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/276 `/scratch/stefan/7770410/working/3D/276' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=N1) `REAL300020113339.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113339 none C=CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 54, 16, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 33, 40, 58, 58, 58, 58, 7, 7, 1, 15, 16, 81, 81, 81, 54, 54, 16, 5, 1, 1, 1, 1, 7, 33, 33, 40, 40, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 464 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113339 none C=CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 85, 31, 31, 31, 12, 12, 12, 7, 7, 7, 1, 1, 1, 1, 1, 8, 10, 16, 16, 16, 16, 1, 1, 7, 31, 31, 115, 115, 115, 85, 85, 31, 12, 7, 7, 7, 7, 1, 8, 8, 10, 10, 7, 7] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 463 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113339 none C=CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 1, 1, 1, 1, 1, 7, 7, 7, 16, 16, 16, 31, 31, 31, 93, 103, 123, 123, 123, 123, 31, 31, 16, 1, 1, 16, 16, 16, 7, 7, 1, 7, 16, 16, 16, 16, 31, 93, 93, 103, 103, 16, 16] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 25, 26] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 473 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113339 none C=CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 122, 122, 122, 88, 88, 88, 66, 66, 66, 24, 24, 24, 7, 4, 1, 1, 1, 1, 1, 1, 24, 24, 66, 122, 122, 201, 201, 201, 201, 201, 122, 88, 66, 66, 66, 66, 24, 7, 7, 4, 4, 66, 66] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 728 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113339 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113339 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113339/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113339/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113339 Building REAL300020113340 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113340' /scratch/stefan/7770410/working/building/REAL300020113340 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113340 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113340/0 /scratch/stefan/7770410/working/building/REAL300020113340 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/277 `/scratch/stefan/7770410/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC=N1) `REAL300020113340.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113340 none CC(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 48, 55, 55, 55, 55, 11, 11, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 11, 33, 33, 48, 48, 1, 1, 21] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 44, 45, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46]) total number of confs: 237 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113340 none CC(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 99, 32, 32, 32, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 32, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 99] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 208 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113340 none CC(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 8, 8, 8, 21, 21, 21, 99, 99, 99, 152, 201, 201, 201, 201, 201, 99, 99, 21, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 21, 21, 21, 21, 99, 152, 152, 201, 201, 21, 21, 1] 201 rigid atoms, others: [1, 3, 4, 5, 46, 24, 25, 26] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 733 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113340 none CC(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 113, 113, 113, 55, 55, 55, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 55, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 113, 55, 55, 55, 55, 10, 6, 6, 4, 4, 55, 55, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 474 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113340 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113340/1 /scratch/stefan/7770410/working/building/REAL300020113340 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 278) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/278 `/scratch/stefan/7770410/working/3D/278' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC=N1) `REAL300020113340.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113340/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113340 none CC(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 48, 55, 55, 55, 55, 11, 11, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 11, 33, 33, 48, 48, 1, 1, 21] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 44, 45, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46]) total number of confs: 237 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113340 none CC(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 99, 32, 32, 32, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 32, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 99] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 208 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113340 none CC(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 8, 8, 8, 21, 21, 21, 99, 99, 99, 152, 201, 201, 201, 201, 201, 99, 99, 21, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 21, 21, 21, 21, 99, 152, 152, 201, 201, 21, 21, 1] 201 rigid atoms, others: [1, 3, 4, 5, 46, 24, 25, 26] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 733 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113340 none CC(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 112, 112, 112, 55, 55, 55, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 55, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 112, 55, 55, 55, 55, 10, 6, 6, 4, 4, 55, 55, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 472 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113340 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113340 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113340/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113340/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113340 Building REAL300020113341 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113341' /scratch/stefan/7770410/working/building/REAL300020113341 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113341 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113341/0 /scratch/stefan/7770410/working/building/REAL300020113341 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/279 `/scratch/stefan/7770410/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C2CC2)N=CS1) `REAL300020113341.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113341 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C2CC2)N=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 5, 5, 5, 1, 1, 1, 1, 1, 8, 11, 13, 13, 13, 13, 1, 1, 5, 21, 54, 54, 75, 75, 54, 54, 54, 21, 5, 5, 5, 5, 1, 8, 8, 11, 11, 5, 5, 75, 75, 75, 75, 75, 54] 133 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 224 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113341 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C2CC2)N=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [21, 6, 21, 21, 44, 44, 44, 75, 75, 75, 111, 133, 133, 133, 133, 133, 75, 75, 44, 6, 1, 1, 1, 1, 6, 6, 6, 21, 44, 44, 44, 44, 75, 111, 111, 133, 133, 44, 44, 1, 1, 1, 1, 1, 6] 133 rigid atoms, others: [39, 40, 41, 42, 43, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44]) total number of confs: 480 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113341 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C2CC2)N=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 36, 36, 36, 15, 15, 15, 8, 4, 1, 1, 1, 1, 1, 1, 15, 15, 36, 72, 118, 118, 133, 133, 118, 118, 118, 72, 36, 36, 36, 36, 15, 8, 8, 4, 4, 36, 36, 133, 133, 133, 133, 133, 118] 133 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 356 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113341 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C2CC2)N=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 21, 29, 34, 34, 34, 34, 5, 5, 1, 6, 27, 27, 44, 44, 27, 27, 27, 6, 1, 1, 1, 1, 5, 21, 21, 29, 29, 1, 1, 44, 44, 44, 44, 44, 27] 133 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 218 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113341 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C2CC2)N=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 27, 27, 27, 54, 54, 54, 93, 114, 117, 117, 117, 117, 54, 54, 27, 1, 1, 1, 6, 6, 1, 1, 1, 11, 27, 27, 27, 27, 54, 93, 93, 114, 114, 27, 27, 6, 6, 6, 6, 6, 1] 133 rigid atoms, others: [1, 44, 19, 20, 21, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 427 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113341 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113341/1 /scratch/stefan/7770410/working/building/REAL300020113341 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 280) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/280 `/scratch/stefan/7770410/working/3D/280' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C2CC2)N=CS1) `REAL300020113341.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113341 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C2CC2)N=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 5, 5, 5, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 5, 21, 53, 53, 74, 74, 53, 53, 53, 21, 5, 5, 5, 5, 1, 8, 8, 10, 10, 5, 5, 74, 74, 74, 74, 74, 53] 131 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 219 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113341 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C2CC2)N=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [19, 6, 19, 19, 42, 42, 42, 74, 74, 74, 109, 131, 131, 131, 131, 131, 74, 74, 42, 6, 1, 1, 1, 1, 6, 6, 6, 19, 42, 42, 42, 42, 74, 109, 109, 131, 131, 42, 42, 1, 1, 1, 1, 1, 6] 131 rigid atoms, others: [39, 40, 41, 42, 43, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44]) total number of confs: 475 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113341 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C2CC2)N=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 35, 35, 35, 14, 14, 14, 8, 4, 1, 1, 1, 1, 1, 1, 14, 14, 35, 70, 116, 116, 131, 131, 116, 116, 116, 70, 35, 35, 35, 35, 14, 8, 8, 4, 4, 35, 35, 131, 131, 131, 131, 131, 116] 131 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 353 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113341 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C2CC2)N=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 21, 29, 35, 35, 35, 35, 5, 5, 1, 6, 26, 26, 42, 42, 26, 26, 26, 6, 1, 1, 1, 1, 5, 21, 21, 29, 29, 1, 1, 42, 42, 42, 42, 42, 26] 131 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 217 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113341 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C2CC2)N=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 26, 26, 26, 53, 53, 53, 92, 112, 116, 116, 116, 116, 53, 53, 26, 1, 1, 1, 6, 6, 1, 1, 1, 10, 26, 26, 26, 26, 53, 92, 92, 112, 112, 26, 26, 6, 6, 6, 6, 6, 1] 131 rigid atoms, others: [1, 44, 19, 20, 21, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 424 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113341 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113341 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113341/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113341/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113341 Building REAL300020113342 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113342' /scratch/stefan/7770410/working/building/REAL300020113342 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113342 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113342/0 /scratch/stefan/7770410/working/building/REAL300020113342 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/281 `/scratch/stefan/7770410/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC=N1) `REAL300020113342.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113342 none COCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 27, 18, 18, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 27, 40, 44, 44, 44, 44, 9, 9, 1, 18, 18, 18, 44, 44, 44, 27, 27, 5, 1, 1, 1, 1, 9, 27, 27, 40, 40, 1, 1, 18] 201 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 268 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113342 none COCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [121, 88, 60, 60, 29, 29, 29, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 60, 60, 60, 121, 121, 121, 88, 88, 29, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 60] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 360 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113342 none COCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 8, 8, 8, 18, 18, 18, 60, 60, 60, 118, 157, 161, 161, 161, 161, 60, 60, 18, 1, 1, 1, 14, 14, 14, 5, 5, 8, 18, 18, 18, 18, 60, 118, 118, 157, 157, 18, 18, 1] 201 rigid atoms, others: [2, 3, 4, 5, 44, 24, 25, 26] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 645 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113342 none COCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 164, 164, 102, 102, 102, 42, 42, 42, 11, 11, 11, 7, 4, 1, 1, 1, 1, 1, 1, 11, 11, 42, 164, 164, 164, 201, 201, 201, 201, 201, 102, 42, 42, 42, 42, 11, 7, 7, 4, 4, 42, 42, 164] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 584 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113342 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113342/1 /scratch/stefan/7770410/working/building/REAL300020113342 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 282) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/282 `/scratch/stefan/7770410/working/3D/282' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC=N1) `REAL300020113342.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113342 none COCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 28, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 27, 40, 44, 44, 44, 44, 9, 9, 1, 19, 19, 19, 46, 46, 46, 28, 28, 6, 1, 1, 1, 1, 9, 27, 27, 40, 40, 1, 1, 19] 201 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 272 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113342 none COCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 90, 62, 62, 30, 30, 30, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 62, 62, 62, 124, 124, 124, 90, 90, 30, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 62] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 365 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113342 none COCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 8, 8, 8, 19, 19, 19, 62, 62, 62, 118, 157, 161, 161, 161, 161, 62, 62, 19, 1, 1, 1, 13, 13, 13, 5, 5, 8, 19, 19, 19, 19, 62, 118, 118, 157, 157, 19, 19, 1] 201 rigid atoms, others: [2, 3, 4, 5, 44, 24, 25, 26] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 639 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113342 none COCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 164, 164, 103, 103, 103, 43, 43, 43, 11, 11, 11, 7, 4, 1, 1, 1, 1, 1, 1, 11, 11, 43, 164, 164, 164, 201, 201, 201, 201, 201, 103, 43, 43, 43, 43, 11, 7, 7, 4, 4, 43, 43, 164] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 585 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113342 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113342 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113342/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113342/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113342 Building REAL300020113343 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113343' /scratch/stefan/7770410/working/building/REAL300020113343 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113343 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113343/0 /scratch/stefan/7770410/working/building/REAL300020113343 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/283 `/scratch/stefan/7770410/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NN=NN1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113343.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113343 none CC(C)C1=NN=NN1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [54, 46, 54, 46, 46, 46, 46, 24, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 8, 8, 5, 5, 1, 54, 54, 54, 54, 54, 54, 54, 24, 24, 5, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1] 70 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 183 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113343 none CC(C)C1=NN=NN1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 70, 70, 70, 70, 43, 15, 15, 15, 5, 5, 5, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 1, 1, 5, 70, 70, 70, 70, 70, 70, 70, 43, 43, 15, 5, 5, 5, 5, 1, 3, 3, 5, 5, 5, 5] 70 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 225 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113343 none CC(C)C1=NN=NN1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 28, 28, 28, 46, 46, 46, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 46, 5, 5, 5, 5, 5, 5, 5, 6, 6, 28, 46, 46, 46, 46, 70, 70, 70, 70, 70, 46, 46] 70 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113343 none CC(C)C1=NN=NN1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 63, 63, 63, 47, 20, 20, 20, 13, 13, 13, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 13, 63, 63, 63, 63, 63, 63, 63, 47, 47, 20, 13, 13, 13, 13, 9, 4, 4, 2, 2, 13, 13] 63 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 204 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113343 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113343/1 /scratch/stefan/7770410/working/building/REAL300020113343 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 284) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/284 `/scratch/stefan/7770410/working/3D/284' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NN=NN1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113343.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113343/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113343 none CC(C)C1=NN=NN1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [54, 46, 54, 46, 46, 46, 46, 24, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 5, 5, 1, 54, 54, 54, 54, 54, 54, 54, 24, 24, 5, 1, 1, 1, 1, 5, 5, 5, 7, 7, 1, 1] 69 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 177 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113343 none CC(C)C1=NN=NN1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 69, 69, 69, 69, 42, 14, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 1, 1, 5, 69, 69, 69, 69, 69, 69, 69, 42, 42, 14, 5, 5, 5, 5, 1, 3, 3, 5, 5, 5, 5] 69 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 218 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113343 none CC(C)C1=NN=NN1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 28, 28, 28, 46, 46, 46, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 46, 5, 5, 5, 5, 5, 5, 5, 6, 6, 28, 46, 46, 46, 46, 69, 69, 69, 69, 69, 46, 46] 69 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113343 none CC(C)C1=NN=NN1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 63, 63, 63, 47, 19, 19, 19, 13, 13, 13, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 13, 63, 63, 63, 63, 63, 63, 63, 47, 47, 19, 13, 13, 13, 13, 9, 4, 4, 2, 2, 13, 13] 63 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 205 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113343 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113343 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113343/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113343/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113343 Building REAL300020113344 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113344' /scratch/stefan/7770410/working/building/REAL300020113344 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113344 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113344/0 /scratch/stefan/7770410/working/building/REAL300020113344 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/285 `/scratch/stefan/7770410/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCCC1) `REAL300020113344.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113344 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 45, 87, 45, 45, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 1, 1, 11, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 45, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 391 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113344 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 144, 201, 144, 144, 69, 69, 69, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 69, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 144, 69, 69, 69, 69, 13, 6, 6, 4, 4, 69, 69, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 730 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113344 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 44, 62, 71, 71, 71, 71, 11, 11, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 11, 44, 44, 62, 62, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 44, 45, 21, 38, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 321 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113344 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 5, 5, 5, 15, 15, 15, 87, 87, 87, 161, 201, 201, 201, 201, 201, 87, 87, 15, 1, 1, 1, 1, 1, 1, 3, 3, 3, 2, 2, 2, 5, 15, 15, 15, 15, 87, 161, 161, 201, 201, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 56, 54, 55, 46, 47, 48, 49, 50, 51, 52, 53, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 755 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113344 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113344/1 /scratch/stefan/7770410/working/building/REAL300020113344 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 286) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/286 `/scratch/stefan/7770410/working/3D/286' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCCC1) `REAL300020113344.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113344/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113344 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 45, 87, 45, 45, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 1, 1, 11, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 45, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 391 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113344 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 144, 201, 144, 144, 69, 69, 69, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 69, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 144, 69, 69, 69, 69, 13, 6, 6, 4, 4, 69, 69, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 730 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113344 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 44, 62, 71, 71, 71, 71, 11, 11, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 11, 44, 44, 62, 62, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 44, 45, 21, 38, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 321 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113344 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 5, 5, 5, 15, 15, 15, 87, 87, 87, 161, 201, 201, 201, 201, 201, 87, 87, 15, 1, 1, 1, 1, 1, 1, 3, 3, 3, 2, 2, 2, 5, 15, 15, 15, 15, 87, 161, 161, 201, 201, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 56, 54, 55, 46, 47, 48, 49, 50, 51, 52, 53, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 755 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113344 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113344 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113344/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113344/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113344 Building REAL300020113345 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113345' /scratch/stefan/7770410/working/building/REAL300020113345 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113345 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113345/0 /scratch/stefan/7770410/working/building/REAL300020113345 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/287 `/scratch/stefan/7770410/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC(=O)N1) `REAL300020113345.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113345 none CCCC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 9, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 7, 7, 7, 19, 31, 31, 31, 31, 31, 7, 7, 1, 9, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 9, 3, 1, 1, 1, 1, 7, 19, 19, 31, 31, 1, 1, 9, 9] 201 rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 47, 48, 40, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50]) total number of confs: 196 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113345 none CCCC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 49, 49, 49, 13, 13, 13, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 49, 49, 49, 49, 97, 97, 97, 97, 97, 97, 97, 49, 13, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7, 49, 49] 201 rigid atoms, others: [42, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 405 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113345 none CCCC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 49, 49, 49, 79, 108, 108, 108, 108, 108, 49, 49, 9, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 5, 9, 9, 9, 9, 49, 79, 79, 108, 108, 9, 9, 1, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 49, 50, 25, 36, 26, 27, 28] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 417 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113345 none CCCC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 108, 108, 108, 41, 41, 41, 32, 32, 32, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 32, 108, 108, 108, 108, 201, 201, 201, 201, 201, 201, 201, 108, 41, 32, 32, 32, 32, 9, 4, 4, 2, 2, 32, 32, 108, 108] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 774 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113345 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113345/1 /scratch/stefan/7770410/working/building/REAL300020113345 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 288) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/288 `/scratch/stefan/7770410/working/3D/288' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC(=O)N1) `REAL300020113345.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113345 none CCCC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 9, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 7, 7, 7, 19, 31, 31, 31, 31, 31, 7, 7, 1, 9, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 9, 3, 1, 1, 1, 1, 7, 19, 19, 31, 31, 1, 1, 9, 9] 201 rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 47, 48, 40, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50]) total number of confs: 196 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113345 none CCCC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 49, 49, 49, 13, 13, 13, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 49, 49, 49, 49, 97, 97, 97, 97, 97, 97, 97, 49, 13, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7, 49, 49] 201 rigid atoms, others: [42, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 405 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113345 none CCCC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 49, 49, 49, 78, 107, 107, 107, 107, 107, 49, 49, 9, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 5, 9, 9, 9, 9, 49, 78, 78, 107, 107, 9, 9, 1, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 49, 50, 25, 36, 26, 27, 28] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 411 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113345 none CCCC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 108, 108, 108, 41, 41, 41, 32, 32, 32, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 32, 108, 108, 108, 108, 201, 201, 201, 201, 201, 201, 201, 108, 41, 32, 32, 32, 32, 9, 4, 4, 2, 2, 32, 32, 108, 108] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 774 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113345 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113345 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113345/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113345/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113345 Building REAL300020113346 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113346' /scratch/stefan/7770410/working/building/REAL300020113346 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113346 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113346/0 /scratch/stefan/7770410/working/building/REAL300020113346 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/289 `/scratch/stefan/7770410/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)OC(C2CC2)=N1) `REAL300020113346.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113346 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)OC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 29, 42, 44, 44, 44, 44, 8, 8, 1, 14, 14, 14, 64, 64, 14, 14, 14, 14, 6, 1, 1, 1, 1, 8, 29, 29, 42, 42, 1, 1, 64, 64, 64, 64, 64] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 42, 21, 41] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47]) total number of confs: 321 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113346 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)OC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 31, 31, 31, 64, 64, 64, 136, 136, 136, 179, 201, 201, 201, 201, 201, 136, 136, 64, 13, 1, 1, 1, 1, 13, 13, 13, 13, 31, 64, 64, 64, 64, 136, 179, 179, 201, 201, 64, 64, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 46, 47, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 648 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113346 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)OC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 28, 28, 28, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 8, 64, 64, 64, 136, 136, 64, 64, 64, 64, 28, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 136, 136, 136, 136, 136] 201 rigid atoms, others: [36, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 390 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113346 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)OC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 14, 14, 14, 64, 64, 64, 130, 168, 168, 168, 168, 168, 64, 64, 14, 1, 1, 1, 13, 13, 1, 2, 2, 2, 3, 14, 14, 14, 14, 64, 130, 130, 168, 168, 14, 14, 13, 13, 13, 13, 13] 201 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 671 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113346 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)OC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [170, 170, 95, 95, 95, 43, 43, 43, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 43, 170, 170, 170, 201, 201, 170, 170, 170, 170, 95, 43, 43, 43, 43, 10, 6, 6, 4, 4, 43, 43, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 528 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113346 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113346/1 /scratch/stefan/7770410/working/building/REAL300020113346 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 290) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/290 `/scratch/stefan/7770410/working/3D/290' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)OC(C2CC2)=N1) `REAL300020113346.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113346 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)OC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 28, 41, 44, 44, 44, 44, 8, 8, 1, 14, 14, 14, 64, 64, 14, 14, 14, 14, 6, 1, 1, 1, 1, 8, 28, 28, 41, 41, 1, 1, 64, 64, 64, 64, 64] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 42, 21, 41] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47]) total number of confs: 320 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113346 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)OC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 32, 32, 32, 64, 64, 64, 136, 136, 136, 180, 201, 201, 201, 201, 201, 136, 136, 64, 13, 1, 1, 1, 1, 13, 13, 13, 13, 32, 64, 64, 64, 64, 136, 180, 180, 201, 201, 64, 64, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 46, 47, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 648 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113346 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)OC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 28, 28, 28, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 8, 65, 65, 65, 136, 136, 65, 65, 65, 65, 28, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 136, 136, 136, 136, 136] 201 rigid atoms, others: [36, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 390 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113346 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)OC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 14, 14, 14, 65, 65, 65, 130, 168, 169, 169, 169, 169, 65, 65, 14, 1, 1, 1, 13, 13, 1, 2, 2, 2, 3, 14, 14, 14, 14, 65, 130, 130, 168, 168, 14, 14, 13, 13, 13, 13, 13] 201 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 671 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113346 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)OC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 95, 95, 95, 43, 43, 43, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 43, 169, 169, 169, 201, 201, 169, 169, 169, 169, 95, 43, 43, 43, 43, 10, 6, 6, 4, 4, 43, 43, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 531 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113346 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113346 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113346/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113346/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113346 Building REAL300020113347 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113347' /scratch/stefan/7770410/working/building/REAL300020113347 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113347 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113347/0 /scratch/stefan/7770410/working/building/REAL300020113347 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/291 `/scratch/stefan/7770410/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)OC(C(C)C)=N1) `REAL300020113347.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113347 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)OC(C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 26, 40, 40, 40, 40, 40, 11, 11, 1, 15, 15, 15, 49, 49, 15, 15, 15, 15, 6, 1, 1, 1, 1, 11, 26, 26, 40, 40, 1, 1, 49, 49, 49, 49, 49, 49, 49] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 42, 21, 41] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 335 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113347 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)OC(C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 47, 47, 47, 11, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 11, 96, 96, 96, 152, 152, 96, 96, 96, 96, 47, 11, 11, 11, 11, 1, 5, 5, 7, 7, 11, 11, 152, 152, 152, 152, 152, 152, 152] 201 rigid atoms, others: [36, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 532 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113347 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)OC(C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 15, 15, 15, 96, 96, 96, 152, 185, 185, 185, 185, 185, 96, 96, 15, 1, 1, 1, 9, 9, 1, 2, 2, 2, 3, 15, 15, 15, 15, 96, 152, 152, 185, 185, 15, 15, 9, 9, 9, 9, 9, 9, 9] 201 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 662 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113347 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)OC(C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [196, 196, 121, 121, 121, 41, 41, 41, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 41, 196, 196, 196, 201, 201, 196, 196, 196, 196, 121, 41, 41, 41, 41, 8, 4, 4, 2, 2, 41, 41, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 493 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113347 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113347/1 /scratch/stefan/7770410/working/building/REAL300020113347 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 292) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/292 `/scratch/stefan/7770410/working/3D/292' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)OC(C(C)C)=N1) `REAL300020113347.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113347 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)OC(C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 26, 40, 40, 40, 40, 40, 11, 11, 1, 15, 15, 15, 49, 49, 15, 15, 15, 15, 6, 1, 1, 1, 1, 11, 26, 26, 40, 40, 1, 1, 49, 49, 49, 49, 49, 49, 49] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 42, 21, 41] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 335 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113347 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)OC(C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 47, 47, 47, 11, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 11, 96, 96, 96, 150, 150, 96, 96, 96, 96, 47, 11, 11, 11, 11, 1, 5, 5, 7, 7, 11, 11, 150, 150, 150, 150, 150, 150, 150] 201 rigid atoms, others: [36, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 523 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113347 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)OC(C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 15, 15, 15, 96, 96, 96, 151, 185, 185, 185, 185, 185, 96, 96, 15, 1, 1, 1, 9, 9, 1, 2, 2, 2, 3, 15, 15, 15, 15, 96, 151, 151, 185, 185, 15, 15, 9, 9, 9, 9, 9, 9, 9] 201 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 662 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113347 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)OC(C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [196, 196, 120, 120, 120, 41, 41, 41, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 41, 196, 196, 196, 201, 201, 196, 196, 196, 196, 120, 41, 41, 41, 41, 7, 4, 4, 2, 2, 41, 41, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 491 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113347 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113347 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113347/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113347/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113347 Building REAL300020113348 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113348' /scratch/stefan/7770410/working/building/REAL300020113348 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113348 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113348/0 /scratch/stefan/7770410/working/building/REAL300020113348 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/293 `/scratch/stefan/7770410/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)OC(CC(C)C)=N1) `REAL300020113348.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113348 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)OC(CC(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 21, 29, 29, 29, 29, 29, 13, 13, 1, 15, 15, 15, 46, 51, 51, 15, 15, 15, 15, 6, 1, 1, 1, 1, 13, 21, 21, 29, 29, 1, 1, 46, 46, 51, 51, 51, 51, 51, 51, 51] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 42, 43, 21] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 298 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113348 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)OC(CC(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 51, 51, 51, 13, 13, 13, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 1, 1, 13, 98, 98, 98, 172, 173, 173, 98, 98, 98, 98, 51, 13, 13, 13, 13, 1, 3, 3, 5, 5, 13, 13, 172, 172, 173, 173, 173, 173, 173, 173, 173] 201 rigid atoms, others: [37, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 638 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113348 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)OC(CC(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 15, 15, 15, 98, 98, 98, 112, 125, 125, 125, 125, 125, 98, 98, 15, 1, 1, 1, 5, 7, 7, 1, 2, 2, 2, 3, 15, 15, 15, 15, 98, 112, 112, 125, 125, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7] 201 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24, 28] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 328 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113348 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)OC(CC(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 81, 81, 81, 30, 30, 30, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 30, 134, 134, 134, 201, 201, 201, 134, 134, 134, 134, 81, 30, 30, 30, 30, 7, 4, 4, 2, 2, 30, 30, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 715 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113348 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113348/1 /scratch/stefan/7770410/working/building/REAL300020113348 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 294) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/294 `/scratch/stefan/7770410/working/3D/294' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)OC(CC(C)C)=N1) `REAL300020113348.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113348 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)OC(CC(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 21, 29, 29, 29, 29, 29, 13, 13, 1, 15, 15, 15, 46, 51, 51, 15, 15, 15, 15, 6, 1, 1, 1, 1, 13, 21, 21, 29, 29, 1, 1, 46, 46, 51, 51, 51, 51, 51, 51, 51] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 42, 43, 21] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 298 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113348 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)OC(CC(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 51, 51, 51, 13, 13, 13, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 1, 1, 13, 97, 97, 97, 172, 173, 173, 97, 97, 97, 97, 51, 13, 13, 13, 13, 1, 3, 3, 5, 5, 13, 13, 172, 172, 173, 173, 173, 173, 173, 173, 173] 201 rigid atoms, others: [37, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 642 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113348 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)OC(CC(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 15, 15, 15, 97, 97, 97, 111, 124, 124, 124, 124, 124, 97, 97, 15, 1, 1, 1, 5, 7, 7, 1, 2, 2, 2, 3, 15, 15, 15, 15, 97, 111, 111, 124, 124, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7] 201 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24, 28] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113348 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)OC(CC(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 81, 81, 81, 31, 31, 31, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 31, 134, 134, 134, 201, 201, 201, 134, 134, 134, 134, 81, 31, 31, 31, 31, 7, 4, 4, 2, 2, 31, 31, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 715 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113348 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113348 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113348/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113348/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113348 Building REAL300020113349 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113349' /scratch/stefan/7770410/working/building/REAL300020113349 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113349 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113349/0 /scratch/stefan/7770410/working/building/REAL300020113349 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/295 `/scratch/stefan/7770410/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1COCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113349.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113349 none CC1=CC=CC=C1COCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 57, 57, 57, 26, 13, 13, 4, 4, 4, 1, 1, 1, 1, 1, 7, 7, 7, 18, 29, 29, 29, 29, 29, 7, 7, 1, 57, 57, 57, 57, 57, 57, 57, 26, 26, 13, 13, 4, 1, 1, 1, 1, 7, 18, 18, 29, 29, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 275 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113349 none CC1=CC=CC=C1COCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [129, 129, 129, 129, 129, 129, 82, 45, 45, 15, 15, 15, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 129, 129, 129, 129, 129, 129, 129, 82, 82, 45, 45, 15, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 439 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113349 none CC1=CC=CC=C1COCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 17, 28, 34, 34, 34, 57, 57, 57, 129, 129, 129, 179, 201, 201, 201, 201, 201, 129, 129, 57, 2, 2, 2, 1, 1, 1, 1, 6, 6, 28, 28, 34, 57, 57, 57, 57, 129, 179, 179, 201, 201, 57, 57] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 34, 35, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 725 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113349 none CC1=CC=CC=C1COCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 145, 87, 85, 39, 39, 39, 29, 29, 29, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 29, 201, 201, 201, 201, 201, 201, 201, 145, 145, 85, 85, 39, 29, 29, 29, 29, 8, 4, 4, 2, 2, 29, 29] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 712 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113349 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113349/1 /scratch/stefan/7770410/working/building/REAL300020113349 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 296) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/296 `/scratch/stefan/7770410/working/3D/296' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1COCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113349.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113349 none CC1=CC=CC=C1COCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 57, 57, 57, 26, 13, 13, 4, 4, 4, 1, 1, 1, 1, 1, 7, 7, 7, 18, 29, 29, 29, 29, 29, 7, 7, 1, 57, 57, 57, 57, 57, 57, 57, 26, 26, 13, 13, 4, 1, 1, 1, 1, 7, 18, 18, 29, 29, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 275 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113349 none CC1=CC=CC=C1COCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [130, 130, 130, 130, 130, 130, 82, 45, 45, 15, 15, 15, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 130, 130, 130, 130, 130, 130, 130, 82, 82, 45, 45, 15, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 440 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113349 none CC1=CC=CC=C1COCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 17, 28, 34, 34, 34, 57, 57, 57, 130, 130, 130, 180, 201, 201, 201, 201, 201, 130, 130, 57, 2, 2, 2, 1, 1, 1, 1, 6, 6, 28, 28, 34, 57, 57, 57, 57, 130, 180, 180, 201, 201, 57, 57] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 34, 35, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 720 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113349 none CC1=CC=CC=C1COCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 145, 87, 85, 39, 39, 39, 29, 29, 29, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 29, 201, 201, 201, 201, 201, 201, 201, 145, 145, 85, 85, 39, 29, 29, 29, 29, 7, 4, 4, 2, 2, 29, 29] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 712 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113349 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113349 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113349/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113349/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113349 Building REAL300020113350 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113350' /scratch/stefan/7770410/working/building/REAL300020113350 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113350 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113350/0 /scratch/stefan/7770410/working/building/REAL300020113350 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/297 `/scratch/stefan/7770410/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1) `REAL300020113350.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113350 none CC1=CC=C([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 25, 25, 25, 116, 116, 116, 144, 164, 164, 164, 164, 164, 116, 116, 25, 5, 5, 5, 5, 5, 5, 1, 1, 8, 25, 25, 25, 25, 116, 144, 144, 164, 164, 25, 25] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 36] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 452 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113350 none CC1=CC=C([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 160, 160, 160, 160, 74, 160, 74, 74, 32, 32, 32, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 32, 201, 201, 201, 201, 201, 201, 160, 160, 74, 32, 32, 32, 32, 9, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 557 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113350 none CC1=CC=C([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 25, 25, 25, 25, 6, 25, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 24, 33, 33, 33, 33, 33, 11, 11, 1, 41, 41, 41, 41, 41, 41, 25, 25, 6, 1, 1, 1, 1, 11, 24, 24, 33, 33, 1, 1] 201 rigid atoms, others: [48, 38, 39, 40, 41, 12, 13, 14, 15, 16, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 216 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113350 none CC1=CC=C([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 16, 41, 41, 41, 153, 153, 153, 187, 201, 201, 201, 201, 201, 153, 153, 41, 1, 2, 2, 2, 1, 1, 5, 5, 16, 41, 41, 41, 41, 153, 187, 187, 201, 201, 41, 41] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 34, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 532 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113350 none CC1=CC=C([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [153, 153, 153, 153, 116, 116, 116, 116, 40, 116, 40, 40, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 11, 153, 153, 153, 153, 153, 153, 116, 116, 40, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 420 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113350 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113350/1 /scratch/stefan/7770410/working/building/REAL300020113350 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 298) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/298 `/scratch/stefan/7770410/working/3D/298' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1) `REAL300020113350.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113350/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113350 none CC1=CC=C([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 25, 25, 25, 116, 116, 116, 144, 165, 165, 165, 165, 165, 116, 116, 25, 5, 5, 5, 5, 5, 5, 1, 1, 8, 25, 25, 25, 25, 116, 144, 144, 165, 165, 25, 25] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 36] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 458 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113350 none CC1=CC=C([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 160, 160, 160, 160, 74, 160, 74, 74, 32, 32, 32, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 32, 201, 201, 201, 201, 201, 201, 160, 160, 74, 32, 32, 32, 32, 9, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 559 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113350 none CC1=CC=C([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 25, 25, 25, 25, 6, 25, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 24, 33, 33, 33, 33, 33, 11, 11, 1, 41, 41, 41, 41, 41, 41, 25, 25, 6, 1, 1, 1, 1, 11, 24, 24, 33, 33, 1, 1] 201 rigid atoms, others: [48, 38, 39, 40, 41, 12, 13, 14, 15, 16, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 216 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113350 none CC1=CC=C([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 16, 41, 41, 41, 153, 153, 153, 186, 201, 201, 201, 201, 201, 153, 153, 41, 1, 2, 2, 2, 1, 1, 5, 5, 16, 41, 41, 41, 41, 153, 186, 186, 201, 201, 41, 41] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 34, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 532 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113350 none CC1=CC=C([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [153, 153, 153, 153, 116, 116, 116, 116, 40, 116, 40, 40, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 11, 153, 153, 153, 153, 153, 153, 116, 116, 40, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 420 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113350 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113350 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113350/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113350/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113350 Building REAL300020113351 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113351' /scratch/stefan/7770410/working/building/REAL300020113351 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113351 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113351/0 /scratch/stefan/7770410/working/building/REAL300020113351 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/299 `/scratch/stefan/7770410/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=CC=C1F) `REAL300020113351.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113351 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 49, 133, 133, 133, 133, 133, 154, 154, 134, 154, 154, 154, 49, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 133, 133, 154, 154, 154, 154] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 537 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113351 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 3, 20, 20, 50, 50, 50, 154, 154, 154, 191, 201, 201, 201, 201, 201, 154, 154, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 154, 191, 191, 201, 201, 50, 50, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [45, 46, 47, 48, 22, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 532 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113351 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 44, 44, 44, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 44, 108, 189, 189, 189, 189, 189, 201, 201, 192, 201, 201, 201, 108, 44, 44, 44, 44, 8, 4, 4, 2, 2, 44, 44, 189, 189, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 636 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113351 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 30, 39, 39, 39, 39, 39, 13, 13, 1, 6, 33, 33, 33, 33, 33, 50, 50, 34, 50, 50, 50, 6, 1, 1, 1, 1, 13, 30, 30, 39, 39, 1, 1, 33, 33, 50, 50, 50, 50] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 41, 42, 34, 18, 35] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48]) total number of confs: 336 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113351 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 33, 33, 33, 133, 133, 133, 170, 184, 184, 184, 184, 184, 133, 133, 33, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 3, 11, 33, 33, 33, 33, 133, 170, 170, 184, 184, 33, 33, 1, 1, 3, 3, 3, 3] 201 rigid atoms, others: [1, 43, 44, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48]) total number of confs: 507 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113351 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113351/1 /scratch/stefan/7770410/working/building/REAL300020113351 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 300) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/300 `/scratch/stefan/7770410/working/3D/300' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=CC=C1F) `REAL300020113351.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113351/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113351 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 49, 133, 133, 133, 133, 133, 153, 153, 134, 153, 153, 153, 49, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 133, 133, 153, 153, 153, 153] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 530 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113351 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 3, 20, 20, 50, 50, 50, 153, 153, 153, 190, 201, 201, 201, 201, 201, 153, 153, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 153, 190, 190, 201, 201, 50, 50, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [45, 46, 47, 48, 22, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 534 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113351 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 44, 44, 44, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 44, 107, 189, 189, 189, 189, 189, 201, 201, 189, 201, 201, 201, 107, 44, 44, 44, 44, 9, 4, 4, 2, 2, 44, 44, 189, 189, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 649 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113351 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 29, 38, 38, 38, 38, 38, 13, 13, 1, 6, 33, 33, 33, 33, 33, 50, 50, 34, 50, 50, 50, 6, 1, 1, 1, 1, 13, 29, 29, 38, 38, 1, 1, 33, 33, 50, 50, 50, 50] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 41, 42, 34, 18, 35] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48]) total number of confs: 333 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113351 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 33, 33, 33, 133, 133, 133, 170, 184, 184, 184, 184, 184, 133, 133, 33, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 3, 11, 33, 33, 33, 33, 133, 170, 170, 184, 184, 33, 33, 1, 1, 3, 3, 3, 3] 201 rigid atoms, others: [1, 43, 44, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48]) total number of confs: 504 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113351 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113351 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113351/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113351/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113351 Building REAL300020113352 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113352' /scratch/stefan/7770410/working/building/REAL300020113352 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113352 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113352/0 /scratch/stefan/7770410/working/building/REAL300020113352 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/301 `/scratch/stefan/7770410/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CNN=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113352.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113352 none O=C(CCC1=CNN=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 27, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 10, 10, 10, 27, 41, 43, 43, 43, 43, 10, 10, 1, 27, 27, 33, 33, 33, 33, 33, 6, 1, 1, 1, 1, 10, 27, 27, 41, 41, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 294 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113352 none O=C(CCC1=CNN=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 93, 105, 105, 105, 105, 105, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 10, 93, 93, 105, 105, 105, 105, 105, 27, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10] 201 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 424 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113352 none O=C(CCC1=CNN=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 4, 2, 1, 1, 1, 1, 1, 1, 19, 19, 37, 37, 37, 122, 122, 122, 177, 201, 201, 201, 201, 201, 122, 122, 37, 4, 4, 2, 2, 1, 1, 1, 19, 37, 37, 37, 37, 122, 177, 177, 201, 201, 37, 37] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 679 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113352 none O=C(CCC1=CNN=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 190, 201, 201, 201, 201, 201, 43, 43, 43, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 43, 190, 190, 201, 201, 201, 201, 201, 85, 43, 43, 43, 43, 9, 5, 5, 3, 3, 43, 43] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 782 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113352 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113352/1 /scratch/stefan/7770410/working/building/REAL300020113352 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 302) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/302 `/scratch/stefan/7770410/working/3D/302' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CNN=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113352.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113352 none O=C(CCC1=CNN=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 27, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 10, 10, 10, 27, 41, 43, 43, 43, 43, 10, 10, 1, 27, 27, 33, 33, 33, 33, 33, 6, 1, 1, 1, 1, 10, 27, 27, 41, 41, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 294 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113352 none O=C(CCC1=CNN=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 93, 105, 105, 105, 105, 105, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 10, 93, 93, 105, 105, 105, 105, 105, 27, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10] 201 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 424 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113352 none O=C(CCC1=CNN=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 4, 2, 1, 1, 1, 1, 1, 1, 19, 19, 37, 37, 37, 122, 122, 122, 177, 201, 201, 201, 201, 201, 122, 122, 37, 4, 4, 2, 2, 1, 1, 1, 19, 37, 37, 37, 37, 122, 177, 177, 201, 201, 37, 37] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 679 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113352 none O=C(CCC1=CNN=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 190, 201, 201, 201, 201, 201, 43, 43, 43, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 43, 190, 190, 201, 201, 201, 201, 201, 85, 43, 43, 43, 43, 9, 5, 5, 3, 3, 43, 43] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 782 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113352 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113352 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113352/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113352/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113352 Building REAL300020113353 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113353' /scratch/stefan/7770410/working/building/REAL300020113353 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113353 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113353/0 /scratch/stefan/7770410/working/building/REAL300020113353 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/303 `/scratch/stefan/7770410/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CNC=N1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113353.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113353 none CC(CC1=CNC=N1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 16, 23, 39, 39, 39, 39, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 30, 44, 50, 50, 50, 50, 10, 10, 1, 16, 16, 16, 16, 23, 23, 39, 39, 39, 6, 1, 1, 1, 1, 10, 30, 30, 44, 44, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 310 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113353 none CC(CC1=CNC=N1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 32, 67, 92, 128, 128, 128, 128, 32, 32, 10, 10, 10, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 10, 67, 67, 67, 67, 92, 92, 128, 128, 128, 32, 10, 10, 10, 10, 1, 5, 5, 7, 7, 10, 10] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 482 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113353 none CC(CC1=CNC=N1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 6, 1, 1, 1, 1, 1, 1, 8, 14, 14, 14, 39, 39, 39, 128, 128, 128, 182, 201, 201, 201, 201, 201, 128, 128, 39, 8, 8, 8, 8, 6, 6, 1, 1, 1, 14, 39, 39, 39, 39, 128, 182, 182, 201, 201, 39, 39] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 35] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 657 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113353 none CC(CC1=CNC=N1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [181, 108, 181, 199, 201, 201, 201, 201, 108, 108, 50, 50, 50, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 50, 181, 181, 181, 181, 199, 199, 201, 201, 201, 108, 50, 50, 50, 50, 10, 6, 6, 4, 4, 50, 50] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 754 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113353 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113353/1 /scratch/stefan/7770410/working/building/REAL300020113353 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 304) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/304 `/scratch/stefan/7770410/working/3D/304' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CNC=N1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113353.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113353/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113353 none CC(CC1=CNC=N1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 16, 23, 40, 40, 40, 40, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 30, 44, 49, 49, 49, 49, 10, 10, 1, 16, 16, 16, 16, 23, 23, 40, 40, 40, 6, 1, 1, 1, 1, 10, 30, 30, 44, 44, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 310 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113353 none CC(CC1=CNC=N1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 32, 66, 90, 128, 128, 128, 128, 32, 32, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 10, 66, 66, 66, 66, 90, 90, 128, 128, 128, 32, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 478 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113353 none CC(CC1=CNC=N1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 6, 1, 1, 1, 1, 1, 1, 8, 15, 15, 15, 40, 40, 40, 128, 128, 128, 181, 201, 201, 201, 201, 201, 128, 128, 40, 8, 8, 8, 8, 6, 6, 1, 1, 1, 15, 40, 40, 40, 40, 128, 181, 181, 201, 201, 40, 40] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 35] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 658 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113353 none CC(CC1=CNC=N1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [181, 107, 181, 199, 201, 201, 201, 201, 107, 107, 49, 49, 49, 9, 9, 9, 6, 4, 1, 1, 1, 1, 1, 1, 9, 9, 49, 181, 181, 181, 181, 199, 199, 201, 201, 201, 107, 49, 49, 49, 49, 9, 6, 6, 4, 4, 49, 49] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 756 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113353 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113353 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113353/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113353/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113353 Building REAL300020113354 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113354' /scratch/stefan/7770410/working/building/REAL300020113354 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113354 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113354/0 /scratch/stefan/7770410/working/building/REAL300020113354 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 305) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/305 `/scratch/stefan/7770410/working/3D/305' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=N1) `REAL300020113354.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113354 none C=CCCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 76, 47, 14, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 26, 33, 42, 42, 42, 42, 7, 7, 1, 14, 14, 102, 102, 102, 76, 76, 47, 47, 14, 5, 1, 1, 1, 1, 7, 26, 26, 33, 33, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 560 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113354 none C=CCCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 99, 69, 24, 24, 24, 12, 12, 12, 7, 7, 7, 1, 1, 1, 1, 1, 8, 10, 14, 14, 14, 14, 1, 1, 7, 24, 24, 124, 124, 124, 99, 99, 69, 69, 24, 12, 7, 7, 7, 7, 1, 8, 8, 10, 10, 7, 7] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 550 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113354 none C=CCCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 14, 8, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 24, 24, 24, 63, 71, 83, 83, 83, 83, 24, 24, 14, 1, 1, 28, 28, 28, 14, 14, 8, 8, 1, 6, 14, 14, 14, 14, 24, 63, 63, 71, 71, 14, 14] 201 rigid atoms, others: [35, 4, 5, 6, 7, 3, 26, 27] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 387 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113354 none C=CCCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 188, 91, 91, 91, 65, 65, 65, 47, 47, 47, 18, 18, 18, 7, 4, 1, 1, 1, 1, 1, 1, 18, 18, 47, 91, 91, 201, 201, 201, 201, 201, 188, 188, 91, 65, 47, 47, 47, 47, 18, 7, 7, 4, 4, 47, 47] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 794 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113354 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113354/1 /scratch/stefan/7770410/working/building/REAL300020113354 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 306) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/306 `/scratch/stefan/7770410/working/3D/306' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=N1) `REAL300020113354.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113354 none C=CCCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 76, 47, 14, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 26, 33, 41, 41, 41, 41, 7, 7, 1, 14, 14, 102, 102, 102, 76, 76, 47, 47, 14, 5, 1, 1, 1, 1, 7, 26, 26, 33, 33, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 558 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113354 none C=CCCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 99, 69, 24, 24, 24, 12, 12, 12, 7, 7, 7, 1, 1, 1, 1, 1, 8, 10, 14, 14, 14, 14, 1, 1, 7, 24, 24, 124, 124, 124, 99, 99, 69, 69, 24, 12, 7, 7, 7, 7, 1, 8, 8, 10, 10, 7, 7] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 550 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113354 none C=CCCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 14, 8, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 24, 24, 24, 64, 72, 83, 83, 83, 83, 24, 24, 14, 1, 1, 28, 28, 28, 14, 14, 8, 8, 1, 6, 14, 14, 14, 14, 24, 64, 64, 72, 72, 14, 14] 201 rigid atoms, others: [35, 4, 5, 6, 7, 3, 26, 27] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 391 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113354 none C=CCCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 188, 91, 91, 91, 65, 65, 65, 47, 47, 47, 18, 18, 18, 7, 4, 1, 1, 1, 1, 1, 1, 18, 18, 47, 91, 91, 201, 201, 201, 201, 201, 188, 188, 91, 65, 47, 47, 47, 47, 18, 7, 7, 4, 4, 47, 47] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 794 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113354 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113354 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113354/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113354/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113354 Building REAL300020113355 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113355' /scratch/stefan/7770410/working/building/REAL300020113355 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113355 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113355/0 /scratch/stefan/7770410/working/building/REAL300020113355 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/307 `/scratch/stefan/7770410/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1CC1) `REAL300020113355.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113355 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 10, 32, 102, 102, 102, 102, 102, 140, 140, 32, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 102, 102, 140, 140, 140, 140, 140] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 445 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113355 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 5, 33, 33, 65, 65, 65, 140, 140, 140, 190, 201, 201, 201, 201, 201, 140, 140, 65, 5, 5, 5, 1, 5, 1, 1, 1, 33, 65, 65, 65, 65, 140, 190, 190, 201, 201, 65, 65, 5, 5, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 22, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 600 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113355 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 36, 36, 36, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 36, 92, 195, 195, 195, 195, 195, 201, 201, 92, 36, 36, 36, 36, 8, 4, 4, 2, 2, 36, 36, 195, 195, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 601 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113355 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 25, 37, 37, 37, 37, 37, 10, 10, 1, 6, 27, 27, 27, 27, 27, 65, 65, 6, 1, 1, 1, 1, 10, 25, 25, 37, 37, 1, 1, 27, 27, 65, 65, 65, 65, 65] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 323 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113355 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 27, 27, 27, 102, 102, 102, 158, 195, 195, 195, 195, 195, 102, 102, 27, 1, 1, 1, 1, 1, 1, 5, 5, 11, 27, 27, 27, 27, 102, 158, 158, 195, 195, 27, 27, 1, 1, 5, 5, 5, 5, 5] 201 rigid atoms, others: [1, 39, 40, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 677 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113355 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113355/1 /scratch/stefan/7770410/working/building/REAL300020113355 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 308) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/308 `/scratch/stefan/7770410/working/3D/308' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1CC1) `REAL300020113355.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113355 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 10, 32, 102, 102, 102, 102, 102, 140, 140, 32, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 102, 102, 140, 140, 140, 140, 140] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 445 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113355 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 5, 33, 33, 65, 65, 65, 140, 140, 140, 190, 201, 201, 201, 201, 201, 140, 140, 65, 5, 5, 5, 1, 5, 1, 1, 1, 33, 65, 65, 65, 65, 140, 190, 190, 201, 201, 65, 65, 5, 5, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 22, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 600 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113355 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 36, 36, 36, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 36, 92, 195, 195, 195, 195, 195, 201, 201, 92, 36, 36, 36, 36, 9, 4, 4, 2, 2, 36, 36, 195, 195, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 599 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113355 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 25, 37, 37, 37, 37, 37, 10, 10, 1, 6, 27, 27, 27, 27, 27, 65, 65, 6, 1, 1, 1, 1, 10, 25, 25, 37, 37, 1, 1, 27, 27, 65, 65, 65, 65, 65] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 323 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113355 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 27, 27, 27, 102, 102, 102, 158, 195, 195, 195, 195, 195, 102, 102, 27, 1, 1, 1, 1, 1, 1, 5, 5, 11, 27, 27, 27, 27, 102, 158, 158, 195, 195, 27, 27, 1, 1, 5, 5, 5, 5, 5] 201 rigid atoms, others: [1, 39, 40, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 677 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113355 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113355 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113355/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113355/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113355 Building REAL300020113356 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113356' /scratch/stefan/7770410/working/building/REAL300020113356 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113356 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113356/0 /scratch/stefan/7770410/working/building/REAL300020113356 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/309 `/scratch/stefan/7770410/working/3D/309' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C[C@@H]1C1=CC=CC=C1) `REAL300020113356.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113356 none C[C@]1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C[C@@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 32, 47, 47, 47, 47, 47, 11, 11, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 11, 32, 32, 47, 47, 1, 1, 18, 18, 18, 18, 18, 18, 18] 201 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 43, 44, 20, 36, 37] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 230 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113356 none C[C@]1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C[C@@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 6, 6, 6, 18, 18, 18, 86, 86, 86, 152, 201, 201, 201, 201, 201, 86, 86, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 18, 18, 18, 18, 86, 152, 152, 201, 201, 18, 18, 2, 2, 1, 1, 1, 1, 1] 201 rigid atoms, others: [47, 48, 49, 50, 51, 22, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 764 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113356 none C[C@]1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C[C@@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 30, 30, 30, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 11, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 30, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 86, 86, 86, 86, 86, 86, 86] 201 rigid atoms, others: [38, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 261 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113356 none C[C@]1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C[C@@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 6, 6, 6, 18, 18, 18, 86, 86, 86, 152, 201, 201, 201, 201, 201, 86, 86, 18, 1, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 2, 6, 18, 18, 18, 18, 86, 152, 152, 201, 201, 18, 18, 1, 1, 2, 2, 1, 2, 2] 201 rigid atoms, others: [0, 1, 2, 45, 46, 21, 22, 23, 24] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51]) total number of confs: 773 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113356 none C[C@]1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C[C@@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 85, 85, 85, 49, 49, 49, 10, 10, 10, 4, 2, 1, 1, 1, 1, 1, 1, 10, 10, 49, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 85, 49, 49, 49, 49, 10, 4, 4, 2, 2, 49, 49, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 576 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113356 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113356/1 /scratch/stefan/7770410/working/building/REAL300020113356 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 310) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/310 `/scratch/stefan/7770410/working/3D/310' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C[C@@H]1C1=CC=CC=C1) `REAL300020113356.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113356 none C[C@]1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C[C@@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 46, 47, 47, 47, 47, 11, 11, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 11, 31, 31, 46, 46, 1, 1, 18, 18, 18, 18, 18, 18, 18] 201 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 43, 44, 20, 36, 37] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 229 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113356 none C[C@]1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C[C@@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 6, 6, 6, 18, 18, 18, 85, 85, 85, 151, 201, 201, 201, 201, 201, 85, 85, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 18, 18, 18, 18, 85, 151, 151, 201, 201, 18, 18, 2, 2, 1, 1, 1, 1, 1] 201 rigid atoms, others: [47, 48, 49, 50, 51, 22, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 763 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113356 none C[C@]1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C[C@@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 29, 29, 29, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 85, 85, 85, 85, 85, 85, 85, 85, 85, 85, 85, 85, 29, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 85, 85, 85, 85, 85, 85, 85] 201 rigid atoms, others: [38, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 263 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113356 none C[C@]1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C[C@@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 6, 6, 6, 18, 18, 18, 85, 85, 85, 151, 201, 201, 201, 201, 201, 85, 85, 18, 1, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 2, 6, 18, 18, 18, 18, 85, 151, 151, 201, 201, 18, 18, 1, 1, 2, 2, 1, 2, 2] 201 rigid atoms, others: [0, 1, 2, 45, 46, 21, 22, 23, 24] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51]) total number of confs: 772 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113356 none C[C@]1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C[C@@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 85, 85, 85, 49, 49, 49, 11, 11, 11, 5, 3, 1, 1, 1, 1, 1, 1, 11, 11, 49, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 85, 49, 49, 49, 49, 11, 5, 5, 3, 3, 49, 49, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 575 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113356 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113356 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113356/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113356/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113356 Building REAL300020113357 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113357' /scratch/stefan/7770410/working/building/REAL300020113357 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113357 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113357/0 /scratch/stefan/7770410/working/building/REAL300020113357 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/311 `/scratch/stefan/7770410/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2CCC[N@@H+]21) `REAL300020113357.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113357 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2CCC[N@@H+]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 9, 9, 9, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 9, 22, 23, 23, 23, 23, 23, 23, 23, 23, 23, 22, 9, 9, 9, 9, 1, 4, 4, 4, 4, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 24 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 73 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113357 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2CCC[N@@H+]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 13, 13, 13, 6, 6, 6, 5, 2, 1, 1, 1, 1, 1, 1, 6, 6, 13, 23, 24, 24, 24, 24, 24, 24, 24, 24, 24, 23, 13, 13, 13, 13, 6, 5, 5, 2, 2, 13, 13, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 24 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 78 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113357 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2CCC[N@@H+]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 11, 11, 11, 11, 11, 11, 9, 9, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 1, 1, 1, 9, 11, 11, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 24 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 38 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113357 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2CCC[N@@H+]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 7, 23, 23, 23, 24, 24, 24, 24, 24, 24, 23, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 7, 7, 7, 23, 24, 24, 24, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 24 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 45 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113357 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113357/1 /scratch/stefan/7770410/working/building/REAL300020113357 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 312) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/312 `/scratch/stefan/7770410/working/3D/312' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2CCC[N@H+]21) `REAL300020113357.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113357 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2CCC[N@H+]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 2, 2, 2, 2, 1, 4, 4, 4, 4, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 5 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 25 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113357 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2CCC[N@H+]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 4, 4, 4, 4, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 2, 2, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 5 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 20 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113357 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2CCC[N@H+]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 2, 2, 1, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 1, 1, 1, 1, 2, 4, 4, 4, 4, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 5 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 22 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113357 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2CCC[N@H+]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 5 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 15 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113357 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113357 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113357/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113357/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113357 Building REAL300020113358 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113358' /scratch/stefan/7770410/working/building/REAL300020113358 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113358 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113358/0 /scratch/stefan/7770410/working/building/REAL300020113358 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/313 `/scratch/stefan/7770410/working/3D/313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1) `REAL300020113358.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113358 none COC1=CC=C(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 48, 47, 53, 53, 31, 12, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 21, 33, 33, 33, 33, 33, 7, 7, 1, 53, 53, 53, 53, 53, 53, 53, 12, 12, 5, 1, 1, 1, 1, 7, 21, 21, 33, 33, 1, 1, 53, 53] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49]) total number of confs: 277 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113358 none COC1=CC=C(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 119, 118, 120, 120, 91, 40, 16, 16, 16, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 120, 120, 120, 120, 120, 120, 120, 40, 40, 16, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7, 120, 120] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 333 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113358 none COC1=CC=C(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 12, 31, 31, 31, 53, 53, 53, 120, 120, 120, 169, 201, 201, 201, 201, 201, 120, 120, 53, 1, 1, 2, 2, 2, 1, 1, 12, 12, 31, 53, 53, 53, 53, 120, 169, 169, 201, 201, 53, 53, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 48, 49, 33, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 735 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113358 none COC1=CC=C(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 199, 103, 53, 53, 53, 33, 33, 33, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 33, 201, 201, 201, 201, 201, 201, 201, 103, 103, 53, 33, 33, 33, 33, 8, 4, 4, 2, 2, 33, 33, 201, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 568 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113358 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113358/1 /scratch/stefan/7770410/working/building/REAL300020113358 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 314) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/314 `/scratch/stefan/7770410/working/3D/314' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1) `REAL300020113358.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113358 none COC1=CC=C(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 48, 47, 53, 53, 31, 12, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 21, 33, 33, 33, 33, 33, 7, 7, 1, 53, 53, 53, 53, 53, 53, 53, 12, 12, 5, 1, 1, 1, 1, 7, 21, 21, 33, 33, 1, 1, 53, 53] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49]) total number of confs: 277 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113358 none COC1=CC=C(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 119, 120, 120, 92, 40, 16, 16, 16, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 120, 120, 120, 120, 120, 120, 120, 40, 40, 16, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7, 120, 120] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 328 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113358 none COC1=CC=C(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 12, 31, 31, 31, 53, 53, 53, 120, 120, 120, 169, 201, 201, 201, 201, 201, 120, 120, 53, 1, 1, 2, 2, 2, 1, 1, 12, 12, 31, 53, 53, 53, 53, 120, 169, 169, 201, 201, 53, 53, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 48, 49, 33, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 736 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113358 none COC1=CC=C(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 199, 103, 53, 53, 53, 33, 33, 33, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 33, 201, 201, 201, 201, 201, 201, 201, 103, 103, 53, 33, 33, 33, 33, 8, 4, 4, 2, 2, 33, 33, 201, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 568 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113358 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113358 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113358/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113358/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113358 Building REAL300020113359 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113359' /scratch/stefan/7770410/working/building/REAL300020113359 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113359 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113359/0 /scratch/stefan/7770410/working/building/REAL300020113359 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/315 `/scratch/stefan/7770410/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020113359.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113359 none CC1=CC=CC(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 40, 40, 22, 11, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 20, 32, 32, 32, 32, 32, 7, 7, 1, 40, 40, 40, 40, 40, 40, 40, 11, 11, 5, 1, 1, 1, 1, 7, 20, 20, 32, 32, 1, 1, 40] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48]) total number of confs: 221 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113359 none CC1=CC=CC(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 103, 103, 60, 32, 16, 16, 16, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 103, 103, 103, 103, 103, 103, 103, 32, 32, 16, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 103] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 278 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113359 none CC1=CC=CC(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 12, 27, 27, 27, 40, 40, 40, 103, 103, 103, 159, 201, 201, 201, 201, 201, 103, 103, 40, 1, 2, 2, 2, 1, 1, 1, 12, 12, 27, 40, 40, 40, 40, 103, 159, 159, 201, 201, 40, 40, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 48, 33, 27, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 784 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113359 none CC1=CC=CC(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 115, 77, 49, 49, 49, 32, 32, 32, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 32, 201, 201, 201, 201, 201, 201, 201, 77, 77, 49, 32, 32, 32, 32, 7, 4, 4, 2, 2, 32, 32, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 533 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113359 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113359/1 /scratch/stefan/7770410/working/building/REAL300020113359 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 316) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/316 `/scratch/stefan/7770410/working/3D/316' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020113359.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113359 none CC1=CC=CC(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 41, 23, 11, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 20, 32, 32, 32, 32, 32, 7, 7, 1, 41, 41, 41, 41, 41, 41, 41, 11, 11, 5, 1, 1, 1, 1, 7, 20, 20, 32, 32, 1, 1, 41] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48]) total number of confs: 223 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113359 none CC1=CC=CC(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 104, 104, 61, 32, 16, 16, 16, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 104, 104, 104, 104, 104, 104, 104, 32, 32, 16, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 104] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 280 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113359 none CC1=CC=CC(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 12, 28, 28, 28, 41, 41, 41, 104, 104, 104, 159, 201, 201, 201, 201, 201, 104, 104, 41, 1, 2, 2, 2, 1, 1, 1, 12, 12, 28, 41, 41, 41, 41, 104, 159, 159, 201, 201, 41, 41, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 48, 33, 27, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 780 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113359 none CC1=CC=CC(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 114, 76, 48, 48, 48, 32, 32, 32, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 32, 201, 201, 201, 201, 201, 201, 201, 76, 76, 48, 32, 32, 32, 32, 7, 4, 4, 2, 2, 32, 32, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 531 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113359 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113359 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113359/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113359/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113359 Building REAL300020113360 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113360' /scratch/stefan/7770410/working/building/REAL300020113360 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113360 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113360/0 /scratch/stefan/7770410/working/building/REAL300020113360 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/317 `/scratch/stefan/7770410/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=CC(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020113360.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113360 none CC1=CC(C)=CC(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 33, 37, 37, 37, 33, 13, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 30, 42, 43, 43, 43, 43, 8, 8, 1, 37, 37, 37, 37, 33, 37, 37, 37, 37, 13, 13, 5, 1, 1, 1, 1, 8, 30, 30, 42, 42, 1, 1, 37] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 51]) total number of confs: 260 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113360 none CC1=CC(C)=CC(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 100, 110, 110, 110, 100, 46, 19, 19, 19, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 110, 110, 110, 110, 100, 110, 110, 110, 110, 46, 46, 19, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 110] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 339 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113360 none CC1=CC(C)=CC(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 8, 18, 18, 18, 37, 37, 37, 108, 108, 108, 168, 201, 201, 201, 201, 201, 108, 108, 37, 1, 2, 2, 2, 1, 2, 2, 2, 1, 8, 8, 18, 37, 37, 37, 37, 108, 168, 168, 201, 201, 37, 37, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 51, 36, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 732 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113360 none CC1=CC(C)=CC(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 196, 201, 201, 201, 196, 130, 74, 74, 74, 43, 43, 43, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 43, 201, 201, 201, 201, 196, 201, 201, 201, 201, 130, 130, 74, 43, 43, 43, 43, 9, 5, 5, 3, 3, 43, 43, 201] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 628 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113360 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113360/1 /scratch/stefan/7770410/working/building/REAL300020113360 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 318) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/318 `/scratch/stefan/7770410/working/3D/318' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=CC(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020113360.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113360 none CC1=CC(C)=CC(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 33, 37, 37, 37, 33, 13, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 30, 42, 43, 43, 43, 43, 8, 8, 1, 37, 37, 37, 37, 33, 37, 37, 37, 37, 13, 13, 5, 1, 1, 1, 1, 8, 30, 30, 42, 42, 1, 1, 37] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 51]) total number of confs: 260 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113360 none CC1=CC(C)=CC(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 100, 110, 110, 110, 100, 46, 19, 19, 19, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 110, 110, 110, 110, 100, 110, 110, 110, 110, 46, 46, 19, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 110] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 339 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113360 none CC1=CC(C)=CC(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 8, 18, 18, 18, 37, 37, 37, 108, 108, 108, 168, 201, 201, 201, 201, 201, 108, 108, 37, 1, 2, 2, 2, 1, 2, 2, 2, 1, 8, 8, 18, 37, 37, 37, 37, 108, 168, 168, 201, 201, 37, 37, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 51, 36, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 731 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113360 none CC1=CC(C)=CC(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 196, 201, 201, 201, 196, 130, 75, 75, 75, 43, 43, 43, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 43, 201, 201, 201, 201, 196, 201, 201, 201, 201, 130, 130, 75, 43, 43, 43, 43, 9, 5, 5, 3, 3, 43, 43, 201] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 626 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113360 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113360 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113360/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113360/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113360 Building REAL300020113361 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113361' /scratch/stefan/7770410/working/building/REAL300020113361 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113361 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113361/0 /scratch/stefan/7770410/working/building/REAL300020113361 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/319 `/scratch/stefan/7770410/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1OCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113361.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113361 none COC1=CC=CC=C1OCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 52, 52, 52, 52, 52, 52, 30, 8, 3, 3, 3, 1, 1, 1, 1, 1, 7, 7, 7, 18, 28, 28, 28, 28, 28, 7, 7, 1, 59, 59, 59, 52, 52, 52, 52, 8, 8, 3, 1, 1, 1, 1, 7, 18, 18, 28, 28, 1, 1] 201 rigid atoms, others: [48, 39, 40, 41, 42, 12, 13, 14, 15, 16, 49, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 222 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113361 none COC1=CC=CC=C1OCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 110, 110, 110, 110, 110, 110, 71, 27, 12, 12, 12, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 118, 118, 118, 110, 110, 110, 110, 27, 27, 12, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [43, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 283 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113361 none COC1=CC=CC=C1OCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 22, 33, 33, 33, 52, 52, 52, 110, 110, 110, 172, 201, 201, 201, 201, 201, 110, 110, 52, 4, 4, 4, 1, 1, 1, 1, 22, 22, 33, 52, 52, 52, 52, 110, 172, 172, 201, 201, 52, 52] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 34, 35, 33] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 774 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113361 none COC1=CC=CC=C1OCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 147, 70, 37, 37, 37, 29, 29, 29, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 29, 201, 201, 201, 201, 201, 201, 201, 70, 70, 37, 29, 29, 29, 29, 7, 4, 4, 2, 2, 29, 29] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 488 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113361 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113361/1 /scratch/stefan/7770410/working/building/REAL300020113361 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 320) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/320 `/scratch/stefan/7770410/working/3D/320' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1OCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113361.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113361/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113361 none COC1=CC=CC=C1OCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 51, 51, 51, 51, 51, 51, 30, 8, 3, 3, 3, 1, 1, 1, 1, 1, 7, 7, 7, 18, 28, 28, 28, 28, 28, 7, 7, 1, 58, 58, 58, 51, 51, 51, 51, 8, 8, 3, 1, 1, 1, 1, 7, 18, 18, 28, 28, 1, 1] 201 rigid atoms, others: [48, 39, 40, 41, 42, 12, 13, 14, 15, 16, 49, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 221 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113361 none COC1=CC=CC=C1OCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 111, 111, 111, 111, 111, 111, 71, 27, 12, 12, 12, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 119, 119, 119, 111, 111, 111, 111, 27, 27, 12, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [43, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 286 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113361 none COC1=CC=CC=C1OCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 22, 33, 33, 33, 51, 51, 51, 111, 111, 111, 173, 201, 201, 201, 201, 201, 111, 111, 51, 4, 4, 4, 1, 1, 1, 1, 22, 22, 33, 51, 51, 51, 51, 111, 173, 173, 201, 201, 51, 51] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 34, 35, 33] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 766 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113361 none COC1=CC=CC=C1OCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 148, 71, 38, 38, 38, 30, 30, 30, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 30, 201, 201, 201, 201, 201, 201, 201, 71, 71, 38, 30, 30, 30, 30, 8, 4, 4, 2, 2, 30, 30] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 488 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113361 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113361 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113361/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113361/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113361 Building REAL300020113362 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113362' /scratch/stefan/7770410/working/building/REAL300020113362 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113362 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113362/0 /scratch/stefan/7770410/working/building/REAL300020113362 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/321 `/scratch/stefan/7770410/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COC1=CC=CC(F)=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113362.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113362 none O=C(COC1=CC=CC(F)=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 11, 26, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 7, 7, 7, 20, 32, 32, 32, 32, 32, 7, 7, 1, 11, 11, 41, 41, 41, 41, 5, 1, 1, 1, 1, 7, 20, 20, 32, 32, 1, 1] 201 rigid atoms, others: [45, 35, 36, 37, 38, 44, 11, 12, 13, 14, 15, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 223 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113362 none O=C(COC1=CC=CC(F)=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 34, 70, 108, 108, 108, 108, 108, 108, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 34, 34, 108, 108, 108, 108, 16, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7] 201 rigid atoms, others: [39, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 294 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113362 none O=C(COC1=CC=CC(F)=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 41, 41, 41, 108, 108, 108, 161, 201, 201, 201, 201, 201, 108, 108, 41, 11, 11, 1, 1, 1, 1, 27, 41, 41, 41, 41, 108, 161, 161, 201, 201, 41, 41] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 746 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113362 none O=C(COC1=CC=CC(F)=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 82, 125, 201, 201, 201, 201, 201, 201, 32, 32, 32, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 32, 82, 82, 201, 201, 201, 201, 50, 32, 32, 32, 32, 8, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 540 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113362 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113362/1 /scratch/stefan/7770410/working/building/REAL300020113362 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 322) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/322 `/scratch/stefan/7770410/working/3D/322' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COC1=CC=CC(F)=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113362.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113362/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113362 none O=C(COC1=CC=CC(F)=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 11, 26, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 7, 7, 7, 20, 32, 32, 32, 32, 32, 7, 7, 1, 11, 11, 41, 41, 41, 41, 5, 1, 1, 1, 1, 7, 20, 20, 32, 32, 1, 1] 201 rigid atoms, others: [45, 35, 36, 37, 38, 44, 11, 12, 13, 14, 15, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 223 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113362 none O=C(COC1=CC=CC(F)=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 35, 71, 109, 109, 109, 109, 109, 109, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 35, 35, 109, 109, 109, 109, 16, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7] 201 rigid atoms, others: [39, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 297 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113362 none O=C(COC1=CC=CC(F)=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 41, 41, 41, 109, 109, 109, 161, 201, 201, 201, 201, 201, 109, 109, 41, 11, 11, 1, 1, 1, 1, 27, 41, 41, 41, 41, 109, 161, 161, 201, 201, 41, 41] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 742 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113362 none O=C(COC1=CC=CC(F)=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 84, 127, 201, 201, 201, 201, 201, 201, 34, 34, 34, 10, 10, 10, 4, 2, 1, 1, 1, 1, 1, 1, 10, 10, 34, 84, 84, 201, 201, 201, 201, 52, 34, 34, 34, 34, 10, 4, 4, 2, 2, 34, 34] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 539 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113362 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113362 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113362/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113362/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113362 Building REAL300020113363 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113363' /scratch/stefan/7770410/working/building/REAL300020113363 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113363 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113363/0 /scratch/stefan/7770410/working/building/REAL300020113363 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/323 `/scratch/stefan/7770410/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C)C(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020113363.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113363 none CC1=CC=C(C)C(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 24, 40, 40, 40, 24, 9, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 20, 32, 32, 32, 32, 32, 7, 7, 1, 40, 40, 40, 40, 24, 40, 40, 40, 40, 9, 9, 5, 1, 1, 1, 1, 7, 20, 20, 32, 32, 1, 1, 40] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 51]) total number of confs: 247 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113363 none CC1=CC=C(C)C(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 82, 113, 113, 113, 82, 26, 15, 15, 15, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 113, 113, 113, 113, 82, 113, 113, 113, 113, 26, 26, 15, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 113] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 347 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113363 none CC1=CC=C(C)C(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 24, 24, 24, 40, 40, 40, 113, 113, 113, 171, 201, 201, 201, 201, 201, 113, 113, 40, 1, 2, 2, 2, 1, 1, 2, 2, 2, 11, 11, 24, 40, 40, 40, 40, 113, 171, 171, 201, 201, 40, 40, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 51, 28, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 754 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113363 none CC1=CC=C(C)C(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 163, 201, 201, 201, 163, 69, 44, 44, 44, 33, 33, 33, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 33, 201, 201, 201, 201, 163, 201, 201, 201, 201, 69, 69, 44, 33, 33, 33, 33, 8, 4, 4, 2, 2, 33, 33, 201] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 584 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113363 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113363/1 /scratch/stefan/7770410/working/building/REAL300020113363 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 324) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/324 `/scratch/stefan/7770410/working/3D/324' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C)C(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020113363.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113363/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113363 none CC1=CC=C(C)C(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 23, 39, 39, 39, 23, 8, 4, 4, 4, 1, 1, 1, 1, 1, 7, 7, 7, 20, 32, 32, 32, 32, 32, 7, 7, 1, 39, 39, 39, 39, 23, 39, 39, 39, 39, 8, 8, 4, 1, 1, 1, 1, 7, 20, 20, 32, 32, 1, 1, 39] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 51]) total number of confs: 245 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113363 none CC1=CC=C(C)C(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 83, 113, 113, 113, 83, 26, 14, 14, 14, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 113, 113, 113, 113, 83, 113, 113, 113, 113, 26, 26, 14, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 113] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 347 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113363 none CC1=CC=C(C)C(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 24, 24, 24, 39, 39, 39, 113, 113, 113, 170, 201, 201, 201, 201, 201, 113, 113, 39, 1, 2, 2, 2, 1, 1, 2, 2, 2, 11, 11, 24, 39, 39, 39, 39, 113, 170, 170, 201, 201, 39, 39, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 51, 28, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 752 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113363 none CC1=CC=C(C)C(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 162, 201, 201, 201, 162, 68, 43, 43, 43, 33, 33, 33, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 33, 201, 201, 201, 201, 162, 201, 201, 201, 201, 68, 68, 43, 33, 33, 33, 33, 8, 4, 4, 2, 2, 33, 33, 201] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 587 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113363 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113363 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113363/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113363/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113363 Building REAL300020113364 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113364' /scratch/stefan/7770410/working/building/REAL300020113364 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113364 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113364/0 /scratch/stefan/7770410/working/building/REAL300020113364 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/325 `/scratch/stefan/7770410/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1C) `REAL300020113364.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113364 none CC1=CC=C(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 44, 44, 22, 11, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 19, 31, 31, 31, 31, 31, 7, 7, 1, 44, 44, 44, 44, 44, 44, 44, 44, 11, 11, 5, 1, 1, 1, 1, 7, 19, 19, 31, 31, 1, 1, 44, 44, 44, 44] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 266 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113364 none CC1=CC=C(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 109, 109, 63, 32, 16, 16, 16, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 109, 109, 109, 109, 109, 109, 109, 109, 32, 32, 16, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 109, 109, 109, 109] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 308 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113364 none CC1=CC=C(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 13, 29, 29, 29, 44, 44, 44, 109, 109, 109, 161, 201, 201, 201, 201, 201, 109, 109, 44, 1, 1, 1, 2, 2, 2, 1, 1, 13, 13, 29, 44, 44, 44, 44, 109, 161, 161, 201, 201, 44, 44, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 48, 26, 27, 28, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51]) total number of confs: 769 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113364 none CC1=CC=C(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 112, 70, 46, 46, 46, 31, 31, 31, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 31, 201, 201, 201, 201, 201, 201, 201, 201, 70, 70, 46, 31, 31, 31, 31, 7, 4, 4, 2, 2, 31, 31, 201, 201, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 516 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113364 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113364/1 /scratch/stefan/7770410/working/building/REAL300020113364 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 326) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/326 `/scratch/stefan/7770410/working/3D/326' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1C) `REAL300020113364.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113364 none CC1=CC=C(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 43, 43, 21, 11, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 19, 31, 31, 31, 31, 31, 7, 7, 1, 43, 43, 43, 43, 43, 43, 43, 43, 11, 11, 5, 1, 1, 1, 1, 7, 19, 19, 31, 31, 1, 1, 43, 43, 43, 43] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 264 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113364 none CC1=CC=C(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 108, 108, 62, 31, 15, 15, 15, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 108, 108, 108, 108, 108, 108, 108, 108, 31, 31, 15, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 108, 108, 108, 108] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 306 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113364 none CC1=CC=C(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 13, 29, 29, 29, 43, 43, 43, 108, 108, 108, 160, 201, 201, 201, 201, 201, 108, 108, 43, 1, 1, 1, 2, 2, 2, 1, 1, 13, 13, 29, 43, 43, 43, 43, 108, 160, 160, 201, 201, 43, 43, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 48, 26, 27, 28, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51]) total number of confs: 771 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113364 none CC1=CC=C(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 112, 70, 46, 46, 46, 31, 31, 31, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 31, 201, 201, 201, 201, 201, 201, 201, 201, 70, 70, 46, 31, 31, 31, 31, 7, 4, 4, 2, 2, 31, 31, 201, 201, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 516 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113364 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113364 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113364/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113364/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113364 Building REAL300020113365 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113365' /scratch/stefan/7770410/working/building/REAL300020113365 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113365 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113365/0 /scratch/stefan/7770410/working/building/REAL300020113365 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/327 `/scratch/stefan/7770410/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(OCCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020113365.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113365 none CC1=CC=CC(OCCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 57, 57, 33, 16, 16, 3, 3, 3, 1, 1, 1, 1, 1, 7, 7, 7, 16, 25, 25, 25, 25, 25, 7, 7, 1, 57, 57, 57, 57, 57, 57, 57, 16, 16, 16, 16, 3, 1, 1, 1, 1, 7, 16, 16, 25, 25, 1, 1, 57] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 51]) total number of confs: 232 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113365 none CC1=CC=CC(OCCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 146, 146, 146, 90, 53, 53, 13, 13, 13, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 146, 146, 146, 146, 146, 146, 146, 53, 53, 53, 53, 13, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 146] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 397 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113365 none CC1=CC=CC(OCCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 10, 23, 37, 37, 37, 57, 57, 57, 146, 146, 146, 179, 201, 201, 201, 201, 201, 146, 146, 57, 1, 2, 2, 2, 1, 1, 1, 10, 10, 23, 23, 37, 57, 57, 57, 57, 146, 179, 179, 201, 201, 57, 57, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 51, 28, 5] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 673 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113365 none CC1=CC=CC(OCCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 120, 83, 83, 33, 33, 33, 31, 31, 31, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 31, 201, 201, 201, 201, 201, 201, 201, 83, 83, 83, 83, 33, 31, 31, 31, 31, 8, 4, 4, 2, 2, 31, 31, 201] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 535 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113365 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113365/1 /scratch/stefan/7770410/working/building/REAL300020113365 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 328) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/328 `/scratch/stefan/7770410/working/3D/328' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(OCCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020113365.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113365 none CC1=CC=CC(OCCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 57, 57, 33, 16, 16, 3, 3, 3, 1, 1, 1, 1, 1, 7, 7, 7, 15, 24, 24, 24, 24, 24, 7, 7, 1, 57, 57, 57, 57, 57, 57, 57, 16, 16, 16, 16, 3, 1, 1, 1, 1, 7, 15, 15, 24, 24, 1, 1, 57] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 51]) total number of confs: 230 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113365 none CC1=CC=CC(OCCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 148, 148, 148, 91, 54, 54, 13, 13, 13, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 148, 148, 148, 148, 148, 148, 148, 54, 54, 54, 54, 13, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 148] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 406 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113365 none CC1=CC=CC(OCCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 10, 22, 37, 37, 37, 57, 57, 57, 148, 148, 148, 179, 201, 201, 201, 201, 201, 148, 148, 57, 1, 2, 2, 2, 1, 1, 1, 10, 10, 22, 22, 37, 57, 57, 57, 57, 148, 179, 179, 201, 201, 57, 57, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 51, 28, 5] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 662 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113365 none CC1=CC=CC(OCCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 121, 82, 82, 32, 32, 32, 30, 30, 30, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 30, 201, 201, 201, 201, 201, 201, 201, 82, 82, 82, 82, 32, 30, 30, 30, 30, 7, 4, 4, 2, 2, 30, 30, 201] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 536 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113365 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113365 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113365/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113365/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113365 Building REAL300020113366 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113366' /scratch/stefan/7770410/working/building/REAL300020113366 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113366 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113366/0 /scratch/stefan/7770410/working/building/REAL300020113366 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/329 `/scratch/stefan/7770410/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCOC1=CC=CC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113366.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113366 none O=C(CCOC1=CC=CC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 20, 21, 39, 40, 40, 39, 40, 40, 1, 1, 1, 1, 1, 7, 7, 7, 21, 32, 32, 32, 32, 32, 7, 7, 1, 20, 20, 21, 21, 40, 40, 39, 40, 40, 5, 1, 1, 1, 1, 7, 21, 21, 32, 32, 1, 1] 201 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 236 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113366 none O=C(CCOC1=CC=CC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 67, 68, 113, 113, 113, 113, 113, 113, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 67, 67, 68, 68, 113, 113, 113, 113, 113, 15, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 354 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113366 none O=C(CCOC1=CC=CC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 10, 4, 3, 1, 1, 1, 1, 1, 1, 1, 22, 23, 40, 40, 40, 113, 113, 113, 163, 201, 201, 201, 201, 201, 113, 113, 40, 10, 10, 4, 4, 1, 1, 1, 1, 1, 22, 40, 40, 40, 40, 113, 163, 163, 201, 201, 40, 40] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 36] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 735 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113366 none O=C(CCOC1=CC=CC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 135, 136, 201, 201, 201, 201, 201, 201, 34, 34, 34, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 34, 135, 135, 136, 136, 201, 201, 201, 201, 201, 46, 34, 34, 34, 34, 9, 4, 4, 2, 2, 34, 34] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 626 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113366 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113366/1 /scratch/stefan/7770410/working/building/REAL300020113366 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 330) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/330 `/scratch/stefan/7770410/working/3D/330' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCOC1=CC=CC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113366.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113366 none O=C(CCOC1=CC=CC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 20, 21, 40, 41, 41, 40, 41, 41, 1, 1, 1, 1, 1, 7, 7, 7, 21, 32, 32, 32, 32, 32, 7, 7, 1, 20, 20, 21, 21, 41, 41, 40, 41, 41, 5, 1, 1, 1, 1, 7, 21, 21, 32, 32, 1, 1] 201 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 238 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113366 none O=C(CCOC1=CC=CC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 67, 68, 113, 113, 113, 113, 113, 113, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 67, 67, 68, 68, 113, 113, 113, 113, 113, 15, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 354 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113366 none O=C(CCOC1=CC=CC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 10, 4, 3, 1, 1, 1, 1, 1, 1, 1, 23, 24, 41, 41, 41, 113, 113, 113, 163, 201, 201, 201, 201, 201, 113, 113, 41, 10, 10, 4, 4, 1, 1, 1, 1, 1, 23, 41, 41, 41, 41, 113, 163, 163, 201, 201, 41, 41] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 36] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 739 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113366 none O=C(CCOC1=CC=CC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 134, 135, 201, 201, 201, 201, 201, 201, 33, 33, 33, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 33, 134, 134, 135, 135, 201, 201, 201, 201, 201, 45, 33, 33, 33, 33, 8, 4, 4, 2, 2, 33, 33] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 623 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113366 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113366 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113366/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113366/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113366 Building REAL300020113367 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113367' /scratch/stefan/7770410/working/building/REAL300020113367 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113367 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113367/0 /scratch/stefan/7770410/working/building/REAL300020113367 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/331 `/scratch/stefan/7770410/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1OCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113367.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113367 none CC1=CC=CC=C1OCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 50, 61, 61, 42, 19, 18, 4, 4, 4, 1, 1, 1, 1, 1, 7, 7, 7, 21, 31, 31, 31, 31, 31, 7, 7, 1, 61, 61, 61, 61, 51, 61, 61, 19, 19, 18, 18, 4, 1, 1, 1, 1, 7, 21, 21, 31, 31, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 296 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113367 none CC1=CC=CC=C1OCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [135, 135, 135, 127, 135, 135, 109, 58, 58, 14, 14, 14, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 135, 135, 135, 135, 127, 135, 135, 58, 58, 58, 58, 14, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 392 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113367 none CC1=CC=CC=C1OCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 24, 42, 42, 42, 61, 61, 61, 135, 135, 135, 188, 201, 201, 201, 201, 201, 135, 135, 61, 2, 2, 2, 1, 1, 1, 1, 11, 11, 24, 24, 42, 61, 61, 61, 61, 135, 188, 188, 201, 201, 61, 61] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 34, 35, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 704 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113367 none CC1=CC=CC=C1OCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 165, 92, 92, 42, 42, 42, 27, 27, 27, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 27, 201, 201, 201, 201, 201, 201, 201, 92, 92, 92, 92, 42, 27, 27, 27, 27, 8, 4, 4, 2, 2, 27, 27] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 540 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113367 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113367/1 /scratch/stefan/7770410/working/building/REAL300020113367 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 332) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/332 `/scratch/stefan/7770410/working/3D/332' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1OCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113367.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113367 none CC1=CC=CC=C1OCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 50, 60, 60, 42, 19, 18, 4, 4, 4, 1, 1, 1, 1, 1, 7, 7, 7, 21, 31, 31, 31, 31, 31, 7, 7, 1, 60, 60, 60, 60, 51, 60, 60, 19, 19, 18, 18, 4, 1, 1, 1, 1, 7, 21, 21, 31, 31, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 291 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113367 none CC1=CC=CC=C1OCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [135, 135, 135, 128, 135, 135, 110, 58, 58, 14, 14, 14, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 135, 135, 135, 135, 128, 135, 135, 58, 58, 58, 58, 14, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 389 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113367 none CC1=CC=CC=C1OCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 24, 41, 41, 41, 60, 60, 60, 135, 135, 135, 188, 201, 201, 201, 201, 201, 135, 135, 60, 2, 2, 2, 1, 1, 1, 1, 11, 11, 24, 24, 41, 60, 60, 60, 60, 135, 188, 188, 201, 201, 60, 60] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 34, 35, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 704 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113367 none CC1=CC=CC=C1OCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 164, 92, 92, 42, 42, 42, 27, 27, 27, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 27, 201, 201, 201, 201, 201, 201, 201, 92, 92, 92, 92, 42, 27, 27, 27, 27, 8, 4, 4, 2, 2, 27, 27] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 540 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113367 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113367 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113367/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113367/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113367 Building REAL300020113368 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113368' /scratch/stefan/7770410/working/building/REAL300020113368 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113368 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113368/0 /scratch/stefan/7770410/working/building/REAL300020113368 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/333 `/scratch/stefan/7770410/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COC1=CC=CC=C1F)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113368.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113368 none O=C(COC1=CC=CC=C1F)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 1, 1, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 12, 34, 62, 62, 37, 62, 62, 62, 1, 1, 1, 1, 1, 7, 7, 7, 21, 33, 33, 33, 33, 33, 7, 7, 1, 12, 12, 62, 62, 53, 62, 4, 1, 1, 1, 1, 7, 21, 21, 33, 33, 1, 1] 201 rigid atoms, others: [45, 35, 36, 37, 38, 44, 11, 12, 13, 14, 15, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 331 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113368 none O=C(COC1=CC=CC=C1F)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 1, 1, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 38, 88, 118, 118, 94, 118, 118, 118, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 38, 38, 118, 118, 112, 118, 14, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7] 201 rigid atoms, others: [39, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 390 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113368 none O=C(COC1=CC=CC=C1F)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 1, 1, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 25, 10, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 62, 62, 62, 118, 118, 118, 173, 201, 201, 201, 201, 201, 118, 118, 62, 25, 25, 1, 1, 1, 1, 41, 62, 62, 62, 62, 118, 173, 173, 201, 201, 62, 62] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 759 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113368 none O=C(COC1=CC=CC=C1F)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 1, 1, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 106, 179, 201, 201, 185, 201, 201, 201, 35, 35, 35, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 35, 106, 106, 201, 201, 201, 201, 49, 35, 35, 35, 35, 9, 4, 4, 2, 2, 35, 35] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 639 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113368 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113368/1 /scratch/stefan/7770410/working/building/REAL300020113368 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 334) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/334 `/scratch/stefan/7770410/working/3D/334' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COC1=CC=CC=C1F)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113368.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113368/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113368 none O=C(COC1=CC=CC=C1F)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 1, 1, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 12, 33, 62, 62, 37, 62, 62, 62, 1, 1, 1, 1, 1, 7, 7, 7, 21, 33, 33, 33, 33, 33, 7, 7, 1, 12, 12, 62, 62, 53, 62, 4, 1, 1, 1, 1, 7, 21, 21, 33, 33, 1, 1] 201 rigid atoms, others: [45, 35, 36, 37, 38, 44, 11, 12, 13, 14, 15, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 332 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113368 none O=C(COC1=CC=CC=C1F)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 1, 1, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 38, 88, 118, 118, 94, 118, 118, 118, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 38, 38, 118, 118, 112, 118, 14, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7] 201 rigid atoms, others: [39, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 390 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113368 none O=C(COC1=CC=CC=C1F)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 1, 1, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 26, 10, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 62, 62, 62, 118, 118, 118, 173, 201, 201, 201, 201, 201, 118, 118, 62, 26, 26, 1, 1, 1, 1, 41, 62, 62, 62, 62, 118, 173, 173, 201, 201, 62, 62] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 758 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113368 none O=C(COC1=CC=CC=C1F)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 1, 1, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 105, 179, 201, 201, 185, 201, 201, 201, 35, 35, 35, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 35, 105, 105, 201, 201, 201, 201, 49, 35, 35, 35, 35, 9, 4, 4, 2, 2, 35, 35] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 638 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113368 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113368 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113368/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113368/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113368 Building REAL300020113369 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113369' /scratch/stefan/7770410/working/building/REAL300020113369 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113369 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113369/0 /scratch/stefan/7770410/working/building/REAL300020113369 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/335 `/scratch/stefan/7770410/working/3D/335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(CCCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1) `REAL300020113369.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113369 none CC1=NOC(CCCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 25, 15, 14, 3, 3, 3, 1, 1, 1, 1, 1, 7, 7, 7, 19, 27, 27, 27, 27, 27, 7, 7, 1, 63, 63, 63, 63, 22, 23, 20, 20, 14, 14, 3, 1, 1, 1, 1, 7, 19, 19, 27, 27, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 293 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113369 none CC1=NOC(CCCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [155, 155, 155, 155, 88, 66, 58, 13, 13, 13, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 155, 155, 155, 155, 81, 81, 80, 80, 58, 58, 13, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 593 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113369 none CC1=NOC(CCCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 16, 25, 44, 44, 44, 63, 63, 63, 155, 155, 155, 187, 201, 201, 201, 201, 201, 155, 155, 63, 1, 2, 2, 2, 8, 8, 16, 16, 25, 25, 44, 63, 63, 63, 63, 155, 187, 187, 201, 201, 63, 63] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 649 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113369 none CC1=NOC(CCCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 132, 94, 97, 38, 38, 38, 29, 29, 29, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 29, 201, 201, 201, 201, 122, 121, 117, 117, 97, 97, 38, 29, 29, 29, 29, 7, 4, 4, 2, 2, 29, 29] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 777 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113369 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113369/1 /scratch/stefan/7770410/working/building/REAL300020113369 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 336) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/336 `/scratch/stefan/7770410/working/3D/336' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(CCCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1) `REAL300020113369.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113369 none CC1=NOC(CCCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 62, 25, 15, 14, 3, 3, 3, 1, 1, 1, 1, 1, 7, 7, 7, 19, 27, 27, 27, 27, 27, 7, 7, 1, 62, 62, 62, 62, 22, 23, 20, 20, 14, 14, 3, 1, 1, 1, 1, 7, 19, 19, 27, 27, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 292 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113369 none CC1=NOC(CCCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [155, 155, 155, 155, 89, 66, 59, 13, 13, 13, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 155, 155, 155, 155, 82, 81, 81, 81, 59, 59, 13, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 599 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113369 none CC1=NOC(CCCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 15, 24, 43, 43, 43, 62, 62, 62, 155, 155, 155, 186, 201, 201, 201, 201, 201, 155, 155, 62, 1, 2, 2, 2, 8, 8, 15, 15, 24, 24, 43, 62, 62, 62, 62, 155, 186, 186, 201, 201, 62, 62] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 647 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113369 none CC1=NOC(CCCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 133, 95, 98, 39, 39, 39, 30, 30, 30, 8, 8, 8, 5, 3, 1, 1, 1, 1, 1, 1, 8, 8, 30, 201, 201, 201, 201, 123, 122, 118, 118, 98, 98, 39, 30, 30, 30, 30, 8, 5, 5, 3, 3, 30, 30] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 778 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113369 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113369 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113369/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113369/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113369 Building REAL300020113370 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113370' /scratch/stefan/7770410/working/building/REAL300020113370 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113370 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113370/0 /scratch/stefan/7770410/working/building/REAL300020113370 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/337 `/scratch/stefan/7770410/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(NC(=O)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NO1) `REAL300020113370.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113370 none CC1=CC(NC(=O)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 14, 13, 6, 14, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 55, 75, 92, 92, 92, 92, 12, 12, 1, 20, 20, 20, 20, 20, 20, 14, 6, 1, 1, 1, 1, 12, 55, 55, 75, 75, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 378 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113370 none CC1=CC(NC(=O)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 79, 78, 50, 79, 50, 50, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 12, 92, 92, 92, 92, 92, 92, 79, 50, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12] 201 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 288 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113370 none CC1=CC(NC(=O)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 7, 8, 8, 20, 20, 20, 92, 92, 92, 157, 201, 201, 201, 201, 201, 92, 92, 20, 1, 1, 2, 2, 2, 1, 4, 8, 20, 20, 20, 20, 92, 157, 157, 201, 201, 20, 20] 201 rigid atoms, others: [0, 1, 2, 3, 4, 26, 27, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 740 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113370 none CC1=CC(NC(=O)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 200, 151, 201, 151, 151, 92, 92, 92, 16, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 92, 201, 201, 201, 201, 201, 201, 201, 151, 92, 92, 92, 92, 16, 6, 6, 4, 4, 92, 92] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 593 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113370 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113370/1 /scratch/stefan/7770410/working/building/REAL300020113370 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 338) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/338 `/scratch/stefan/7770410/working/3D/338' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(NC(=O)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NO1) `REAL300020113370.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113370/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113370 none CC1=CC(NC(=O)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 14, 13, 6, 14, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 55, 75, 92, 92, 92, 92, 12, 12, 1, 20, 20, 20, 20, 20, 20, 14, 6, 1, 1, 1, 1, 12, 55, 55, 75, 75, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 378 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113370 none CC1=CC(NC(=O)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 79, 78, 50, 79, 50, 50, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 12, 92, 92, 92, 92, 92, 92, 79, 50, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12] 201 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 288 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113370 none CC1=CC(NC(=O)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 7, 8, 8, 20, 20, 20, 92, 92, 92, 157, 201, 201, 201, 201, 201, 92, 92, 20, 1, 1, 2, 2, 2, 1, 4, 8, 20, 20, 20, 20, 92, 157, 157, 201, 201, 20, 20] 201 rigid atoms, others: [0, 1, 2, 3, 4, 26, 27, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 740 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113370 none CC1=CC(NC(=O)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 200, 151, 201, 151, 151, 92, 92, 92, 16, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 92, 201, 201, 201, 201, 201, 201, 201, 151, 92, 92, 92, 92, 16, 6, 6, 4, 4, 92, 92] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 593 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113370 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113370 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113370/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113370/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113370 Building REAL300020113371 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113371' /scratch/stefan/7770410/working/building/REAL300020113371 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113371 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113371/0 /scratch/stefan/7770410/working/building/REAL300020113371 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/339 `/scratch/stefan/7770410/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C)=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(=O)N1) `REAL300020113371.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113371 none CC1=NC(C)=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 26, 26, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 33, 47, 49, 49, 49, 49, 9, 9, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 9, 33, 33, 47, 47, 1, 1, 26] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49]) total number of confs: 281 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113371 none CC1=NC(C)=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 100, 100, 100, 31, 31, 31, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 10, 10, 10, 10, 1, 1, 9, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 31, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9, 100] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 385 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113371 none CC1=NC(C)=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 9, 9, 9, 26, 26, 26, 100, 100, 100, 174, 201, 201, 201, 201, 201, 100, 100, 26, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 9, 26, 26, 26, 26, 100, 174, 174, 201, 201, 26, 26, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 49, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 732 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113371 none CC1=NC(C)=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 110, 110, 110, 49, 49, 49, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 49, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 110, 49, 49, 49, 49, 10, 5, 5, 3, 3, 49, 49, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 748 number of broken/clashed sets: 200 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113371 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113371/1 /scratch/stefan/7770410/working/building/REAL300020113371 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 340) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/340 `/scratch/stefan/7770410/working/3D/340' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C)=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(=O)N1) `REAL300020113371.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113371/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113371 none CC1=NC(C)=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 26, 26, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 33, 47, 49, 49, 49, 49, 9, 9, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 9, 33, 33, 47, 47, 1, 1, 26] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49]) total number of confs: 281 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113371 none CC1=NC(C)=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 100, 100, 100, 31, 31, 31, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 10, 10, 10, 10, 1, 1, 9, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 31, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9, 100] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 385 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113371 none CC1=NC(C)=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 9, 9, 9, 26, 26, 26, 100, 100, 100, 174, 201, 201, 201, 201, 201, 100, 100, 26, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 9, 26, 26, 26, 26, 100, 174, 174, 201, 201, 26, 26, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 49, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 732 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113371 none CC1=NC(C)=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 110, 110, 110, 49, 49, 49, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 49, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 110, 49, 49, 49, 49, 10, 5, 5, 3, 3, 49, 49, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 748 number of broken/clashed sets: 200 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113371 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113371 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113371/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113371/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113371 Building REAL300020113372 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113372' /scratch/stefan/7770410/working/building/REAL300020113372 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113372 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113372/0 /scratch/stefan/7770410/working/building/REAL300020113372 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/341 `/scratch/stefan/7770410/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(=O)NC1=O) `REAL300020113372.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113372 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 61, 80, 102, 102, 102, 102, 13, 13, 1, 20, 20, 20, 20, 19, 20, 20, 20, 20, 6, 1, 1, 1, 1, 13, 61, 61, 80, 80, 1, 1, 20] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 384 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113372 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 52, 52, 52, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 18, 18, 18, 18, 1, 1, 13, 91, 91, 91, 91, 84, 91, 91, 91, 91, 52, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13, 91] 201 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 253 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113372 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 8, 20, 20, 20, 91, 91, 91, 158, 201, 201, 201, 201, 201, 91, 91, 20, 1, 1, 1, 1, 1, 2, 2, 2, 1, 8, 20, 20, 20, 20, 91, 158, 158, 201, 201, 20, 20, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 44, 23, 24, 25, 26, 27, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 732 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113372 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 189, 189, 189, 102, 102, 102, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 102, 201, 201, 201, 201, 201, 201, 201, 201, 201, 189, 102, 102, 102, 102, 18, 6, 6, 4, 4, 102, 102, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 547 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113372 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113372/1 /scratch/stefan/7770410/working/building/REAL300020113372 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 342) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/342 `/scratch/stefan/7770410/working/3D/342' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(=O)NC1=O) `REAL300020113372.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113372 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 61, 80, 102, 102, 102, 102, 13, 13, 1, 21, 21, 21, 21, 20, 21, 21, 21, 21, 6, 1, 1, 1, 1, 13, 61, 61, 80, 80, 1, 1, 21] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 382 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113372 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 54, 54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 17, 17, 17, 17, 1, 1, 13, 95, 95, 95, 95, 88, 95, 95, 95, 95, 54, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13, 95] 201 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 257 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113372 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 8, 21, 21, 21, 95, 95, 95, 164, 201, 201, 201, 201, 201, 95, 95, 21, 1, 1, 1, 1, 1, 2, 2, 2, 1, 8, 21, 21, 21, 21, 95, 164, 164, 201, 201, 21, 21, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 44, 23, 24, 25, 26, 27, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 712 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113372 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 189, 189, 189, 102, 102, 102, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 102, 201, 201, 201, 201, 201, 201, 201, 201, 201, 189, 102, 102, 102, 102, 17, 6, 6, 4, 4, 102, 102, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 549 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113372 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113372 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113372/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113372/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113372 Building REAL300020113373 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113373' /scratch/stefan/7770410/working/building/REAL300020113373 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113373 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113373/0 /scratch/stefan/7770410/working/building/REAL300020113373 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/343 `/scratch/stefan/7770410/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NN(C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113373.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113373 none CC(C)C1=NN(C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 32, 47, 55, 55, 55, 55, 11, 11, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 32, 32, 47, 47, 1, 1] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 235 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113373 none CC(C)C1=NN(C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 106, 106, 106, 106, 106, 33, 33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 11, 11, 11, 11, 1, 1, 11, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 33, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 219 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113373 none CC(C)C1=NN(C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 22, 22, 22, 106, 106, 106, 156, 201, 201, 201, 201, 201, 106, 106, 22, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 1, 7, 22, 22, 22, 22, 106, 156, 156, 201, 201, 22, 22] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 34, 38, 5, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 704 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113373 none CC(C)C1=NN(C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 111, 111, 111, 55, 55, 55, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 55, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 111, 55, 55, 55, 55, 11, 6, 6, 4, 4, 55, 55] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 472 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113373 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113373/1 /scratch/stefan/7770410/working/building/REAL300020113373 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 344) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/344 `/scratch/stefan/7770410/working/3D/344' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NN(C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113373.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113373 none CC(C)C1=NN(C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 32, 47, 55, 55, 55, 55, 11, 11, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 32, 32, 47, 47, 1, 1] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 235 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113373 none CC(C)C1=NN(C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 106, 106, 106, 106, 106, 33, 33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 33, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 217 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113373 none CC(C)C1=NN(C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 22, 22, 22, 106, 106, 106, 156, 201, 201, 201, 201, 201, 106, 106, 22, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 1, 7, 22, 22, 22, 22, 106, 156, 156, 201, 201, 22, 22] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 34, 38, 5, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 707 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113373 none CC(C)C1=NN(C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 112, 112, 112, 56, 56, 56, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 56, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 112, 56, 56, 56, 56, 12, 6, 6, 4, 4, 56, 56] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 472 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113373 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113373 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113373/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113373/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113373 Building REAL300020113374 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113374' /scratch/stefan/7770410/working/building/REAL300020113374 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113374 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113374/0 /scratch/stefan/7770410/working/building/REAL300020113374 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/345 `/scratch/stefan/7770410/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=NC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113374.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113374 none CN(C)C1=NC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 16, 18, 16, 16, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 39, 56, 70, 70, 70, 70, 11, 11, 1, 18, 18, 18, 18, 18, 18, 16, 16, 16, 6, 1, 1, 1, 1, 11, 39, 39, 56, 56, 1, 1] 201 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 288 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113374 none CN(C)C1=NC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 88, 90, 88, 88, 88, 88, 88, 38, 38, 38, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 11, 90, 90, 90, 90, 90, 90, 88, 88, 88, 38, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 225 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113374 none CN(C)C1=NC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 88, 88, 88, 164, 200, 201, 201, 201, 201, 88, 88, 16, 4, 4, 4, 4, 4, 4, 1, 1, 1, 5, 16, 16, 16, 16, 88, 164, 164, 200, 200, 16, 16] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 35, 36] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 730 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113374 none CN(C)C1=NC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 122, 122, 122, 74, 74, 74, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 74, 201, 201, 201, 201, 201, 201, 201, 201, 201, 122, 74, 74, 74, 74, 15, 6, 6, 4, 4, 74, 74] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 467 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113374 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113374/1 /scratch/stefan/7770410/working/building/REAL300020113374 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 346) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/346 `/scratch/stefan/7770410/working/3D/346' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=NC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113374.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113374 none CN(C)C1=NC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 16, 18, 16, 16, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 40, 57, 72, 72, 72, 72, 11, 11, 1, 18, 18, 18, 18, 18, 18, 16, 16, 16, 6, 1, 1, 1, 1, 11, 40, 40, 57, 57, 1, 1] 201 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 293 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113374 none CN(C)C1=NC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 88, 90, 88, 88, 88, 88, 88, 38, 38, 38, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 11, 90, 90, 90, 90, 90, 90, 88, 88, 88, 38, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 225 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113374 none CN(C)C1=NC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 88, 88, 88, 164, 200, 201, 201, 201, 201, 88, 88, 16, 4, 4, 4, 4, 4, 4, 1, 1, 1, 5, 16, 16, 16, 16, 88, 164, 164, 200, 200, 16, 16] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 35, 36] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 733 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113374 none CN(C)C1=NC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 123, 123, 123, 73, 73, 73, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 73, 201, 201, 201, 201, 201, 201, 201, 201, 201, 123, 73, 73, 73, 73, 14, 6, 6, 4, 4, 73, 73] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 472 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113374 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113374 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113374/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113374/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113374 Building REAL300020113375 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113375' /scratch/stefan/7770410/working/building/REAL300020113375 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113375 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113375/0 /scratch/stefan/7770410/working/building/REAL300020113375 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/347 `/scratch/stefan/7770410/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CNC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113375.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113375 none CC1=CNC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 37, 55, 69, 69, 69, 69, 11, 11, 1, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 11, 37, 37, 55, 55, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40]) total number of confs: 282 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113375 none CC1=CNC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 97, 97, 97, 42, 42, 42, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 11, 97, 97, 97, 97, 97, 97, 42, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11] 201 rigid atoms, others: [36, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 222 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113375 none CC1=CNC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 19, 19, 97, 97, 97, 159, 201, 201, 201, 201, 201, 97, 97, 19, 2, 2, 2, 1, 1, 1, 7, 19, 19, 19, 19, 97, 159, 159, 201, 201, 19, 19] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 729 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113375 none CC1=CNC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 136, 136, 136, 69, 69, 69, 16, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 69, 201, 201, 201, 201, 201, 201, 136, 69, 69, 69, 69, 16, 6, 6, 4, 4, 69, 69] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 488 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113375 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113375/1 /scratch/stefan/7770410/working/building/REAL300020113375 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 348) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/348 `/scratch/stefan/7770410/working/3D/348' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CNC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113375.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113375/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113375 none CC1=CNC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 36, 53, 67, 67, 67, 67, 11, 11, 1, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 11, 36, 36, 53, 53, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40]) total number of confs: 275 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113375 none CC1=CNC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 99, 99, 42, 42, 42, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 11, 99, 99, 99, 99, 99, 99, 42, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11] 201 rigid atoms, others: [36, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 225 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113375 none CC1=CNC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 20, 20, 20, 99, 99, 99, 159, 201, 201, 201, 201, 201, 99, 99, 20, 2, 2, 2, 1, 1, 1, 7, 20, 20, 20, 20, 99, 159, 159, 201, 201, 20, 20] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 723 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113375 none CC1=CNC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 134, 134, 134, 68, 68, 68, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 68, 201, 201, 201, 201, 201, 201, 134, 68, 68, 68, 68, 14, 6, 6, 4, 4, 68, 68] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 488 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113375 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113375 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113375/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113375/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113375 Building REAL300020113376 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113376' /scratch/stefan/7770410/working/building/REAL300020113376 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113376 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113376/0 /scratch/stefan/7770410/working/building/REAL300020113376 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/349 `/scratch/stefan/7770410/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=NN2C=CC=NC2=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113376.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113376 none O=C(CC1=NN2C=CC=NC2=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 1, 1, 8, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 36, 94, 94, 94, 94, 94, 94, 94, 94, 1, 1, 1, 1, 1, 7, 7, 7, 42, 48, 69, 69, 69, 69, 7, 7, 1, 36, 36, 94, 94, 94, 6, 1, 1, 1, 1, 7, 42, 42, 48, 48, 1, 1] 201 rigid atoms, others: [45, 35, 36, 37, 38, 44, 12, 13, 14, 15, 16, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 411 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113376 none O=C(CC1=NN2C=CC=NC2=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 1, 1, 8, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 71, 136, 136, 136, 136, 136, 136, 136, 136, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 19, 19, 19, 19, 1, 1, 7, 71, 71, 136, 136, 136, 28, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7] 201 rigid atoms, others: [39, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 397 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113376 none O=C(CC1=NN2C=CC=NC2=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 1, 1, 8, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 55, 94, 94, 94, 136, 136, 136, 200, 201, 201, 201, 201, 201, 136, 136, 94, 8, 8, 1, 1, 1, 54, 94, 94, 94, 94, 136, 200, 200, 201, 201, 94, 94] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 663 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113376 none O=C(CC1=NN2C=CC=NC2=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 1, 1, 8, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 128, 160, 201, 201, 201, 201, 201, 201, 201, 201, 76, 76, 76, 32, 32, 32, 8, 4, 1, 1, 1, 1, 1, 1, 32, 32, 76, 160, 160, 201, 201, 201, 128, 76, 76, 76, 76, 32, 8, 8, 4, 4, 76, 76] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 593 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113376 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113376/1 /scratch/stefan/7770410/working/building/REAL300020113376 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 350) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/350 `/scratch/stefan/7770410/working/3D/350' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=NN2C=CC=NC2=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113376.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113376/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113376 none O=C(CC1=NN2C=CC=NC2=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 1, 1, 8, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 36, 96, 96, 96, 96, 96, 96, 96, 96, 1, 1, 1, 1, 1, 7, 7, 7, 42, 48, 69, 69, 69, 69, 7, 7, 1, 36, 36, 96, 96, 96, 6, 1, 1, 1, 1, 7, 42, 42, 48, 48, 1, 1] 201 rigid atoms, others: [45, 35, 36, 37, 38, 44, 12, 13, 14, 15, 16, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 413 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113376 none O=C(CC1=NN2C=CC=NC2=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 1, 1, 8, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 71, 137, 137, 137, 137, 137, 137, 137, 137, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 19, 19, 19, 19, 1, 1, 7, 71, 71, 137, 137, 137, 28, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7] 201 rigid atoms, others: [39, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 398 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113376 none O=C(CC1=NN2C=CC=NC2=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 1, 1, 8, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 55, 96, 96, 96, 137, 137, 137, 200, 201, 201, 201, 201, 201, 137, 137, 96, 8, 8, 1, 1, 1, 54, 96, 96, 96, 96, 137, 200, 200, 201, 201, 96, 96] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 662 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113376 none O=C(CC1=NN2C=CC=NC2=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 1, 1, 8, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [126, 126, 126, 159, 201, 201, 201, 201, 201, 201, 201, 201, 75, 75, 75, 31, 31, 31, 8, 4, 1, 1, 1, 1, 1, 1, 31, 31, 75, 159, 159, 201, 201, 201, 126, 75, 75, 75, 75, 31, 8, 8, 4, 4, 75, 75] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 598 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113376 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113376 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113376/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113376/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113376 Building REAL300020113377 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113377' /scratch/stefan/7770410/working/building/REAL300020113377 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113377 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113377/0 /scratch/stefan/7770410/working/building/REAL300020113377 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/351 `/scratch/stefan/7770410/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1) `REAL300020113377.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113377 none CN1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 5, 5, 5, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 3, 3, 1, 10, 10, 10, 10, 10, 10, 5, 1, 1, 1, 1, 3, 5, 5, 5, 5, 1, 1] 12 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 40, 41, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) total number of confs: 35 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113377 none CN1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 3, 10, 10, 10, 10, 10, 10, 7, 3, 3, 3, 3, 1, 5, 5, 5, 5, 3, 3] 12 rigid atoms, others: [35, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 39 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113377 none CN1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12, 12, 10, 10, 10, 1, 2, 2, 2, 1, 1, 6, 10, 10, 10, 10, 10, 12, 12, 12, 12, 10, 10] 12 rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113377 none CN1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 9, 9, 9, 5, 5, 5, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 12, 9, 5, 5, 5, 5, 5, 3, 3, 1, 1, 5, 5] 12 rigid atoms, others: [38, 39, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 32 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113377 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113377/1 /scratch/stefan/7770410/working/building/REAL300020113377 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 352) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/352 `/scratch/stefan/7770410/working/3D/352' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1) `REAL300020113377.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113377/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113377 none CN1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 5, 5, 5, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 3, 3, 1, 10, 10, 10, 10, 10, 10, 5, 1, 1, 1, 1, 3, 5, 5, 5, 5, 1, 1] 12 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 40, 41, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) total number of confs: 35 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113377 none CN1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 3, 10, 10, 10, 10, 10, 10, 7, 3, 3, 3, 3, 1, 5, 5, 5, 5, 3, 3] 12 rigid atoms, others: [35, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 39 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113377 none CN1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12, 12, 10, 10, 10, 1, 2, 2, 2, 1, 1, 6, 10, 10, 10, 10, 10, 12, 12, 12, 12, 10, 10] 12 rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113377 none CN1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 9, 9, 9, 5, 5, 5, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 12, 9, 5, 5, 5, 5, 5, 3, 3, 1, 1, 5, 5] 12 rigid atoms, others: [38, 39, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 32 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113377 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113377 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113377/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113377/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113377 Building REAL300020113378 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113378' /scratch/stefan/7770410/working/building/REAL300020113378 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113378 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113378/0 /scratch/stefan/7770410/working/building/REAL300020113378 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/353 `/scratch/stefan/7770410/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=CN=CC=C21) `REAL300020113378.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113378 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=CN=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 10, 10, 10, 10, 1, 1, 11, 32, 91, 91, 91, 91, 91, 91, 91, 91, 91, 32, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 91, 91, 91, 91, 91, 91] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 196 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113378 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=CN=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 47, 47, 47, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 47, 86, 201, 201, 201, 201, 201, 201, 201, 201, 201, 86, 47, 47, 47, 47, 10, 5, 5, 3, 3, 47, 47, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 409 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113378 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=CN=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 46, 47, 47, 47, 47, 11, 11, 1, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 11, 31, 31, 46, 46, 1, 1, 19, 19, 19, 19, 19, 19] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113378 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=CN=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 19, 19, 19, 91, 91, 91, 159, 201, 201, 201, 201, 201, 91, 91, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 19, 91, 159, 159, 201, 201, 19, 19, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 754 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113378 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113378/1 /scratch/stefan/7770410/working/building/REAL300020113378 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 354) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/354 `/scratch/stefan/7770410/working/3D/354' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=CN=CC=C21) `REAL300020113378.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113378/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113378 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=CN=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 10, 10, 10, 10, 1, 1, 11, 32, 91, 91, 91, 91, 91, 91, 91, 91, 91, 32, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 91, 91, 91, 91, 91, 91] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 196 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113378 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=CN=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 48, 48, 48, 11, 11, 11, 5, 3, 1, 1, 1, 1, 1, 1, 11, 11, 48, 87, 201, 201, 201, 201, 201, 201, 201, 201, 201, 87, 48, 48, 48, 48, 11, 5, 5, 3, 3, 48, 48, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 409 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113378 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=CN=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 46, 47, 47, 47, 47, 11, 11, 1, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 11, 31, 31, 46, 46, 1, 1, 19, 19, 19, 19, 19, 19] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113378 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=CN=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 19, 19, 19, 91, 91, 91, 159, 201, 201, 201, 201, 201, 91, 91, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 19, 91, 159, 159, 201, 201, 19, 19, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 754 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113378 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113378 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113378/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113378/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113378 Building REAL300020113379 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113379' /scratch/stefan/7770410/working/building/REAL300020113379 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113379 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113379/0 /scratch/stefan/7770410/working/building/REAL300020113379 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/355 `/scratch/stefan/7770410/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=NC2=NN1) `REAL300020113379.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113379 none CC1=C2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=NC2=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 28, 41, 45, 45, 45, 45, 9, 9, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 9, 28, 28, 41, 41, 1, 1, 14, 14] 201 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46]) total number of confs: 200 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113379 none CC1=C2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=NC2=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 26, 26, 26, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 71, 71, 71, 71, 71, 71, 71, 71, 71, 26, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 71, 71] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 166 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113379 none CC1=C2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=NC2=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 71, 71, 71, 146, 201, 201, 201, 201, 201, 71, 71, 14, 1, 1, 1, 1, 1, 2, 2, 2, 1, 5, 14, 14, 14, 14, 71, 146, 146, 201, 201, 14, 14, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 45, 46, 24, 25, 26, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 826 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113379 none CC1=C2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=NC2=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 82, 82, 82, 46, 46, 46, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 46, 201, 201, 201, 201, 201, 201, 201, 201, 201, 82, 46, 46, 46, 46, 11, 6, 6, 4, 4, 46, 46, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 417 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113379 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113379/1 /scratch/stefan/7770410/working/building/REAL300020113379 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 356) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/356 `/scratch/stefan/7770410/working/3D/356' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=NC2=NN1) `REAL300020113379.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113379/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113379 none CC1=C2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=NC2=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 28, 41, 45, 45, 45, 45, 9, 9, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 9, 28, 28, 41, 41, 1, 1, 14, 14] 201 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46]) total number of confs: 200 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113379 none CC1=C2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=NC2=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 26, 26, 26, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 71, 71, 71, 71, 71, 71, 71, 71, 71, 26, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 71, 71] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 166 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113379 none CC1=C2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=NC2=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 71, 71, 71, 146, 201, 201, 201, 201, 201, 71, 71, 14, 1, 1, 1, 1, 1, 2, 2, 2, 1, 5, 14, 14, 14, 14, 71, 146, 146, 201, 201, 14, 14, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 45, 46, 24, 25, 26, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 826 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113379 none CC1=C2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=NC2=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 81, 81, 81, 45, 45, 45, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 45, 201, 201, 201, 201, 201, 201, 201, 201, 201, 81, 45, 45, 45, 45, 10, 6, 6, 4, 4, 45, 45, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 416 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113379 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113379 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113379/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113379/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113379 Building REAL300020113380 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113380' /scratch/stefan/7770410/working/building/REAL300020113380 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113380 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113380/0 /scratch/stefan/7770410/working/building/REAL300020113380 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/357 `/scratch/stefan/7770410/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(C2=COC=C2)=NN1) `REAL300020113380.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113380 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(C2=COC=C2)=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 12, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 36, 43, 43, 43, 91, 91, 91, 91, 43, 43, 36, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 43, 91, 91, 91, 43] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 226 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113380 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(C2=COC=C2)=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 12, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 7, 12, 12, 25, 25, 25, 91, 91, 91, 153, 201, 201, 201, 201, 201, 91, 91, 25, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 12, 25, 25, 25, 25, 91, 153, 153, 201, 201, 25, 25, 7, 1, 1, 1, 7] 201 rigid atoms, others: [42, 43, 44, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45]) total number of confs: 752 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113380 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(C2=COC=C2)=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 12, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 53, 53, 53, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 53, 106, 106, 106, 106, 201, 201, 201, 201, 106, 106, 106, 53, 53, 53, 53, 12, 6, 6, 4, 4, 53, 53, 106, 201, 201, 201, 106] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 490 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113380 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(C2=COC=C2)=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 12, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 32, 47, 52, 52, 52, 52, 11, 11, 1, 6, 10, 10, 10, 25, 25, 25, 25, 10, 10, 6, 1, 1, 1, 1, 11, 32, 32, 47, 47, 1, 1, 10, 25, 25, 25, 10] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113380 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(C2=COC=C2)=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 12, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 10, 10, 10, 43, 43, 43, 81, 106, 106, 106, 106, 106, 43, 43, 10, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 5, 10, 10, 10, 10, 43, 81, 81, 106, 106, 10, 10, 1, 7, 7, 7, 1] 201 rigid atoms, others: [1, 41, 45, 19, 20, 21, 22, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 412 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113380 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113380/1 /scratch/stefan/7770410/working/building/REAL300020113380 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 358) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/358 `/scratch/stefan/7770410/working/3D/358' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(C2=COC=C2)=NN1) `REAL300020113380.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113380 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(C2=COC=C2)=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 12, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 36, 43, 43, 43, 91, 91, 91, 91, 43, 43, 36, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 43, 91, 91, 91, 43] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 224 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113380 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(C2=COC=C2)=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 12, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 7, 12, 12, 26, 26, 26, 91, 91, 91, 153, 201, 201, 201, 201, 201, 91, 91, 26, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 12, 26, 26, 26, 26, 91, 153, 153, 201, 201, 26, 26, 7, 1, 1, 1, 7] 201 rigid atoms, others: [42, 43, 44, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45]) total number of confs: 754 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113380 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(C2=COC=C2)=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 12, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 53, 53, 53, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 53, 107, 107, 107, 107, 201, 201, 201, 201, 107, 107, 107, 53, 53, 53, 53, 12, 6, 6, 4, 4, 53, 53, 107, 201, 201, 201, 107] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 490 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113380 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(C2=COC=C2)=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 12, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 46, 51, 51, 51, 51, 11, 11, 1, 6, 11, 11, 11, 26, 26, 26, 26, 11, 11, 6, 1, 1, 1, 1, 11, 31, 31, 46, 46, 1, 1, 11, 26, 26, 26, 11] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113380 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(C2=COC=C2)=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 12, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 11, 11, 11, 43, 43, 43, 81, 107, 107, 107, 107, 107, 43, 43, 11, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 5, 11, 11, 11, 11, 43, 81, 81, 107, 107, 11, 11, 1, 7, 7, 7, 1] 201 rigid atoms, others: [1, 41, 45, 19, 20, 21, 22, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 421 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113380 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113380 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113380/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113380/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113380 Building REAL300020113381 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113381' /scratch/stefan/7770410/working/building/REAL300020113381 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113381 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113381/0 /scratch/stefan/7770410/working/building/REAL300020113381 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/359 `/scratch/stefan/7770410/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C(C)CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=C1) `REAL300020113381.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113381 none CC1=NN(C(C)CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 25, 17, 25, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 38, 51, 60, 60, 60, 60, 9, 9, 1, 36, 36, 36, 36, 36, 36, 25, 25, 25, 25, 17, 17, 6, 1, 1, 1, 1, 9, 38, 38, 51, 51, 1, 1, 36, 36, 36, 36] 201 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 48, 49, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50, 51, 52, 53]) total number of confs: 344 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113381 none CC1=NN(C(C)CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 81, 57, 81, 30, 30, 30, 9, 9, 9, 1, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 1, 1, 9, 107, 107, 107, 107, 107, 107, 81, 81, 81, 81, 57, 57, 30, 9, 9, 9, 9, 1, 9, 9, 11, 11, 9, 9, 107, 107, 107, 107] 201 rigid atoms, others: [43, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 434 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113381 none CC1=NN(C(C)CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 7, 17, 17, 17, 36, 36, 36, 107, 107, 107, 178, 201, 201, 201, 201, 201, 107, 107, 36, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 7, 7, 17, 36, 36, 36, 36, 107, 178, 178, 201, 201, 36, 36, 2, 2, 2, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 53, 26, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 743 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113381 none CC1=NN(C(C)CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 178, 201, 127, 127, 127, 60, 60, 60, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 60, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 178, 178, 127, 60, 60, 60, 60, 13, 6, 6, 4, 4, 60, 60, 201, 201, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 744 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113381 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113381/1 /scratch/stefan/7770410/working/building/REAL300020113381 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 360) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/360 `/scratch/stefan/7770410/working/3D/360' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C(C)CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=C1) `REAL300020113381.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113381 none CC1=NN(C(C)CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 26, 17, 26, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 38, 51, 60, 60, 60, 60, 9, 9, 1, 37, 37, 37, 37, 37, 37, 26, 26, 26, 26, 17, 17, 6, 1, 1, 1, 1, 9, 38, 38, 51, 51, 1, 1, 37, 37, 37, 37] 201 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 48, 49, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50, 51, 52, 53]) total number of confs: 350 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113381 none CC1=NN(C(C)CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 81, 57, 81, 30, 30, 30, 9, 9, 9, 1, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 1, 1, 9, 107, 107, 107, 107, 107, 107, 81, 81, 81, 81, 57, 57, 30, 9, 9, 9, 9, 1, 9, 9, 11, 11, 9, 9, 107, 107, 107, 107] 201 rigid atoms, others: [43, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 434 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113381 none CC1=NN(C(C)CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 7, 18, 18, 18, 37, 37, 37, 107, 107, 107, 177, 201, 201, 201, 201, 201, 107, 107, 37, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 7, 7, 18, 37, 37, 37, 37, 107, 177, 177, 201, 201, 37, 37, 2, 2, 2, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 53, 26, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 744 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113381 none CC1=NN(C(C)CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 178, 201, 127, 127, 127, 60, 60, 60, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 60, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 178, 178, 127, 60, 60, 60, 60, 13, 6, 6, 4, 4, 60, 60, 201, 201, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 742 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113381 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113381 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113381/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113381/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113381 Building REAL300020113382 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113382' /scratch/stefan/7770410/working/building/REAL300020113382 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113382 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113382/0 /scratch/stefan/7770410/working/building/REAL300020113382 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/361 `/scratch/stefan/7770410/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=C(CCC2)NC1=O) `REAL300020113382.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113382 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=C(CCC2)NC1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 17, 17, 17, 17, 1, 1, 12, 51, 95, 95, 95, 95, 95, 95, 95, 95, 95, 51, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 95, 95, 95, 95, 95, 95, 95, 95] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 249 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113382 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=C(CCC2)NC1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 106, 106, 106, 20, 20, 20, 6, 4, 1, 1, 1, 1, 1, 1, 20, 20, 106, 189, 201, 201, 201, 201, 201, 201, 201, 201, 201, 189, 106, 106, 106, 106, 20, 6, 6, 4, 4, 106, 106, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 536 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113382 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=C(CCC2)NC1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 66, 84, 105, 105, 105, 105, 12, 12, 1, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 12, 66, 66, 84, 84, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 389 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113382 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=C(CCC2)NC1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 20, 20, 20, 95, 95, 95, 165, 201, 201, 201, 201, 201, 95, 95, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 20, 20, 20, 20, 95, 165, 165, 201, 201, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 714 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113382 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113382/1 /scratch/stefan/7770410/working/building/REAL300020113382 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 362) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/362 `/scratch/stefan/7770410/working/3D/362' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=C(CCC2)NC1=O) `REAL300020113382.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113382 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=C(CCC2)NC1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 18, 18, 18, 18, 1, 1, 12, 51, 94, 94, 94, 94, 94, 94, 94, 94, 94, 51, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 94, 94, 94, 94, 94, 94, 94, 94] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 249 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113382 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=C(CCC2)NC1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 105, 105, 105, 21, 21, 21, 6, 4, 1, 1, 1, 1, 1, 1, 21, 21, 105, 189, 201, 201, 201, 201, 201, 201, 201, 201, 201, 189, 105, 105, 105, 105, 21, 6, 6, 4, 4, 105, 105, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 541 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113382 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=C(CCC2)NC1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 65, 83, 104, 104, 104, 104, 12, 12, 1, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 12, 65, 65, 83, 83, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 386 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113382 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=C(CCC2)NC1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 20, 20, 20, 94, 94, 94, 165, 201, 201, 201, 201, 201, 94, 94, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 20, 20, 20, 20, 94, 165, 165, 201, 201, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 719 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113382 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113382 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113382/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113382/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113382 Building REAL300020113383 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113383' /scratch/stefan/7770410/working/building/REAL300020113383 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300020113383 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113383/0 /scratch/stefan/7770410/working/building/REAL300020113383 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/363 `/scratch/stefan/7770410/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=CN1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113383.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113383 none CC1=NC=CN1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 45, 29, 5, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 27, 39, 41, 41, 41, 41, 10, 10, 1, 45, 45, 45, 45, 45, 29, 29, 5, 1, 1, 1, 1, 10, 27, 27, 39, 39, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 282 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113383 none CC1=NC=CN1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 120, 120, 120, 92, 21, 21, 21, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 10, 120, 120, 120, 120, 120, 92, 92, 21, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10] 201 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 406 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113383 none CC1=NC=CN1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 25, 25, 25, 45, 45, 45, 120, 120, 120, 175, 201, 201, 201, 201, 201, 120, 120, 45, 2, 2, 2, 1, 1, 5, 5, 25, 45, 45, 45, 45, 120, 175, 175, 201, 201, 45, 45] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 666 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113383 none CC1=NC=CN1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 165, 68, 68, 68, 42, 42, 42, 11, 11, 11, 7, 4, 1, 1, 1, 1, 1, 1, 11, 11, 42, 201, 201, 201, 201, 201, 165, 165, 68, 42, 42, 42, 42, 11, 7, 7, 4, 4, 42, 42] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 685 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113383 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113383/1 /scratch/stefan/7770410/working/building/REAL300020113383 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 364) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/364 `/scratch/stefan/7770410/working/3D/364' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=CN1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113383.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113383/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113383 none CC1=NC=CN1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 45, 29, 5, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 27, 39, 41, 41, 41, 41, 10, 10, 1, 45, 45, 45, 45, 45, 29, 29, 5, 1, 1, 1, 1, 10, 27, 27, 39, 39, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 282 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113383 none CC1=NC=CN1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 120, 120, 120, 92, 21, 21, 21, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 10, 120, 120, 120, 120, 120, 92, 92, 21, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10] 201 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 406 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113383 none CC1=NC=CN1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 25, 25, 25, 45, 45, 45, 120, 120, 120, 175, 201, 201, 201, 201, 201, 120, 120, 45, 2, 2, 2, 1, 1, 5, 5, 25, 45, 45, 45, 45, 120, 175, 175, 201, 201, 45, 45] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 666 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113383 none CC1=NC=CN1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 165, 68, 68, 68, 42, 42, 42, 11, 11, 11, 7, 4, 1, 1, 1, 1, 1, 1, 11, 11, 42, 201, 201, 201, 201, 201, 165, 165, 68, 42, 42, 42, 42, 11, 7, 7, 4, 4, 42, 42] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 685 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113383 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `2' /scratch/stefan/7770410/working/building/REAL300020113383/2 /scratch/stefan/7770410/working/building/REAL300020113383 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 2 (index: 365) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/365 `/scratch/stefan/7770410/working/3D/365' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=[NH+]C=CN1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113383.mol2' -> `2.mol2' `temp.mol2' -> `REAL300020113383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113383/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113383 none CC1=[NH+]C=CN1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 100, 100, 100, 44, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 12, 12, 12, 12, 12, 12, 11, 11, 1, 100, 100, 100, 100, 100, 44, 44, 6, 1, 1, 1, 1, 11, 12, 12, 12, 12, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 44, 10, 11, 12, 13, 14, 45, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 241 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113383 none CC1=[NH+]C=CN1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 139, 37, 37, 37, 11, 11, 11, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 11, 201, 201, 201, 201, 201, 139, 139, 37, 11, 11, 11, 11, 1, 4, 4, 4, 4, 11, 11] 201 rigid atoms, others: [39, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 612 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113383 none CC1=[NH+]C=CN1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 100, 100, 100, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 100, 2, 2, 2, 1, 1, 8, 8, 50, 100, 100, 100, 100, 201, 201, 201, 201, 201, 100, 100] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 439 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113383 none CC1=[NH+]C=CN1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 140, 38, 38, 38, 12, 12, 12, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 201, 201, 201, 201, 201, 140, 140, 38, 12, 12, 12, 12, 4, 3, 3, 1, 1, 12, 12] 201 rigid atoms, others: [42, 43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45]) total number of confs: 608 number of broken/clashed sets: 7 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113383 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113383 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 2: /scratch/stefan/7770410/working/building/REAL300020113383/2.* 1: /scratch/stefan/7770410/working/building/REAL300020113383/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113383/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113383 Building REAL300020113384 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113384' /scratch/stefan/7770410/working/building/REAL300020113384 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113384 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113384/0 /scratch/stefan/7770410/working/building/REAL300020113384 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/366 `/scratch/stefan/7770410/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NNC2=C1CCCCC2) `REAL300020113384.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113384 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NNC2=C1CCCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 19, 19, 19, 19, 1, 1, 12, 51, 88, 88, 88, 88, 88, 88, 88, 88, 88, 51, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 244 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113384 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NNC2=C1CCCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [198, 198, 110, 110, 110, 21, 21, 21, 6, 4, 1, 1, 1, 1, 1, 1, 21, 21, 110, 198, 201, 201, 201, 201, 201, 201, 201, 201, 201, 198, 110, 110, 110, 110, 21, 6, 6, 4, 4, 110, 110, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 545 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113384 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NNC2=C1CCCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 65, 84, 109, 109, 109, 109, 12, 12, 1, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 12, 65, 65, 84, 84, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 396 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113384 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NNC2=C1CCCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 16, 16, 16, 88, 88, 88, 165, 201, 201, 201, 201, 201, 88, 88, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 16, 16, 16, 16, 88, 165, 165, 201, 201, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 719 number of broken/clashed sets: 201 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113384 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113384/1 /scratch/stefan/7770410/working/building/REAL300020113384 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 367) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/367 `/scratch/stefan/7770410/working/3D/367' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NNC2=C1CCCCC2) `REAL300020113384.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113384 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NNC2=C1CCCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 19, 19, 19, 19, 1, 1, 12, 51, 88, 88, 88, 88, 88, 88, 88, 88, 88, 51, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 245 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113384 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NNC2=C1CCCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [198, 198, 109, 109, 109, 22, 22, 22, 6, 4, 1, 1, 1, 1, 1, 1, 22, 22, 109, 198, 201, 201, 201, 201, 201, 201, 201, 201, 201, 198, 109, 109, 109, 109, 22, 6, 6, 4, 4, 109, 109, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 548 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113384 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NNC2=C1CCCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 65, 84, 109, 109, 109, 109, 12, 12, 1, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 12, 65, 65, 84, 84, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 395 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113384 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NNC2=C1CCCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 15, 15, 15, 88, 88, 88, 165, 201, 201, 201, 201, 201, 88, 88, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 15, 15, 15, 15, 88, 165, 165, 201, 201, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 719 number of broken/clashed sets: 201 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113384 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113384 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113384/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113384/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113384 Building REAL300020113385 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113385' /scratch/stefan/7770410/working/building/REAL300020113385 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300020113385 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113385/0 /scratch/stefan/7770410/working/building/REAL300020113385 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/368 `/scratch/stefan/7770410/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN1CCOCC1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113385.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113385 none CC(CN1CCOCC1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 6, 21, 29, 29, 29, 29, 29, 29, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 28, 42, 44, 44, 44, 44, 9, 9, 1, 21, 21, 21, 21, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 9, 28, 28, 42, 42, 1, 1] 201 rigid atoms, others: [11, 15, 44, 43, 12, 13, 14, 45, 52, 46, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 293 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113385 none CC(CN1CCOCC1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 24, 85, 101, 101, 101, 101, 101, 101, 24, 24, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 85, 85, 85, 85, 101, 101, 101, 101, 101, 101, 101, 101, 101, 101, 24, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [14, 47, 16, 17, 18, 25, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 430 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113385 none CC(CN1CCOCC1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 3, 1, 1, 1, 1, 1, 1, 1, 4, 13, 13, 13, 29, 29, 29, 101, 101, 101, 159, 201, 201, 201, 201, 201, 101, 101, 29, 4, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 13, 29, 29, 29, 29, 101, 159, 159, 201, 201, 29, 29] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 41, 39, 2, 40, 35, 36, 38, 37] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 741 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113385 none CC(CN1CCOCC1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [198, 81, 198, 201, 201, 201, 201, 201, 201, 81, 81, 44, 44, 44, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 44, 198, 198, 198, 198, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 81, 44, 44, 44, 44, 10, 6, 6, 4, 4, 44, 44] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 737 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113385 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113385/1 /scratch/stefan/7770410/working/building/REAL300020113385 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 369) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/369 `/scratch/stefan/7770410/working/3D/369' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C[NH+]1CCOCC1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113385.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113385 none CC(C[NH+]1CCOCC1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 16, 25, 26, 26, 26, 26, 26, 26, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 12, 12, 12, 12, 12, 12, 10, 10, 1, 16, 16, 16, 16, 25, 25, 26, 26, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 10, 12, 12, 12, 12, 1, 1] 56 rigid atoms, others: [45, 44, 12, 13, 14, 15, 16, 46, 54, 47, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50, 51, 52]) total number of confs: 126 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113385 none CC(C[NH+]1CCOCC1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [50, 30, 50, 53, 55, 55, 55, 55, 55, 55, 30, 30, 10, 10, 10, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 10, 50, 50, 50, 50, 53, 53, 55, 55, 55, 55, 55, 55, 55, 55, 30, 10, 10, 10, 10, 1, 4, 4, 4, 4, 10, 10] 56 rigid atoms, others: [48, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54]) total number of confs: 216 number of broken/clashed sets: 12 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113385 none CC(C[NH+]1CCOCC1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [6, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 26, 26, 26, 55, 55, 55, 56, 56, 56, 56, 56, 56, 55, 55, 26, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 13, 26, 26, 26, 26, 55, 56, 56, 56, 56, 26, 26] 56 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 42, 39, 40, 35, 41, 36, 38, 37] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 132 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113385 none CC(C[NH+]1CCOCC1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [52, 32, 52, 55, 56, 56, 56, 56, 56, 56, 32, 32, 12, 12, 12, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 52, 52, 52, 52, 55, 55, 56, 56, 56, 56, 56, 56, 56, 56, 32, 12, 12, 12, 12, 4, 3, 3, 1, 1, 12, 12] 56 rigid atoms, others: [19, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 53, 54]) total number of confs: 211 number of broken/clashed sets: 12 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113385 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `2' /scratch/stefan/7770410/working/building/REAL300020113385/2 /scratch/stefan/7770410/working/building/REAL300020113385 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 2 (index: 370) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/370 `/scratch/stefan/7770410/working/3D/370' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN1CCOCC1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113385.mol2' -> `2.mol2' `temp.mol2' -> `REAL300020113385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113385/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113385 none CC(CN1CCOCC1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 6, 21, 29, 29, 29, 29, 29, 29, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 28, 42, 44, 44, 44, 44, 9, 9, 1, 21, 21, 21, 21, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 9, 28, 28, 42, 42, 1, 1] 201 rigid atoms, others: [11, 15, 44, 43, 12, 13, 14, 45, 52, 46, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 293 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113385 none CC(CN1CCOCC1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 24, 85, 101, 101, 101, 101, 101, 101, 24, 24, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 85, 85, 85, 85, 101, 101, 101, 101, 101, 101, 101, 101, 101, 101, 24, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [14, 47, 16, 17, 18, 25, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 430 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113385 none CC(CN1CCOCC1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 3, 1, 1, 1, 1, 1, 1, 1, 4, 13, 13, 13, 29, 29, 29, 101, 101, 101, 159, 201, 201, 201, 201, 201, 101, 101, 29, 4, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 13, 29, 29, 29, 29, 101, 159, 159, 201, 201, 29, 29] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 41, 39, 2, 40, 35, 36, 38, 37] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 741 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113385 none CC(CN1CCOCC1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [198, 81, 198, 201, 201, 201, 201, 201, 201, 81, 81, 44, 44, 44, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 44, 198, 198, 198, 198, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 81, 44, 44, 44, 44, 10, 6, 6, 4, 4, 44, 44] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 737 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113385 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113385 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 2: /scratch/stefan/7770410/working/building/REAL300020113385/2.* 1: /scratch/stefan/7770410/working/building/REAL300020113385/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113385/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113385 Building REAL300020113386 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113386' /scratch/stefan/7770410/working/building/REAL300020113386 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113386 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113386/0 /scratch/stefan/7770410/working/building/REAL300020113386 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/371 `/scratch/stefan/7770410/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1) `REAL300020113386.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113386 none CC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 12, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 20, 30, 30, 30, 30, 30, 7, 7, 1, 26, 26, 26, 26, 26, 26, 26, 12, 12, 5, 1, 1, 1, 1, 7, 20, 20, 30, 30, 1, 1, 26] 201 rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 11, 12, 45, 44, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46]) total number of confs: 189 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113386 none CC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 56, 20, 20, 20, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 107, 107, 107, 107, 107, 107, 107, 56, 56, 20, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 107] 201 rigid atoms, others: [39, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 325 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113386 none CC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 26, 26, 26, 107, 107, 107, 166, 201, 201, 201, 201, 201, 107, 107, 26, 1, 1, 2, 2, 2, 1, 1, 7, 7, 13, 26, 26, 26, 26, 107, 166, 166, 201, 201, 26, 26, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 46, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 714 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113386 none CC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 117, 51, 51, 51, 32, 32, 32, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 32, 201, 201, 201, 201, 201, 201, 201, 117, 117, 51, 32, 32, 32, 32, 8, 4, 4, 2, 2, 32, 32, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 614 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113386 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113386/1 /scratch/stefan/7770410/working/building/REAL300020113386 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 372) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/372 `/scratch/stefan/7770410/working/3D/372' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1) `REAL300020113386.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113386 none CC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 12, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 20, 30, 30, 30, 30, 30, 7, 7, 1, 26, 26, 26, 26, 26, 26, 26, 12, 12, 5, 1, 1, 1, 1, 7, 20, 20, 30, 30, 1, 1, 26] 201 rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 11, 12, 45, 44, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46]) total number of confs: 189 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113386 none CC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 106, 56, 20, 20, 20, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 106, 106, 106, 106, 106, 106, 106, 56, 56, 20, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 106] 201 rigid atoms, others: [39, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 324 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113386 none CC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 26, 26, 26, 106, 106, 106, 165, 201, 201, 201, 201, 201, 106, 106, 26, 1, 1, 2, 2, 2, 1, 1, 7, 7, 13, 26, 26, 26, 26, 106, 165, 165, 201, 201, 26, 26, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 46, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 722 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113386 none CC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 117, 51, 51, 51, 31, 31, 31, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 31, 201, 201, 201, 201, 201, 201, 201, 117, 117, 51, 31, 31, 31, 31, 8, 4, 4, 2, 2, 31, 31, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 614 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113386 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113386 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113386/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113386/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113386 Building REAL300020113387 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113387' /scratch/stefan/7770410/working/building/REAL300020113387 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113387 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113387/0 /scratch/stefan/7770410/working/building/REAL300020113387 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/373 `/scratch/stefan/7770410/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CSC2=NC=CN12)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113387.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113387 none O=C(CC1=CSC2=NC=CN12)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 8, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 21, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 8, 8, 8, 22, 34, 34, 34, 34, 34, 8, 8, 1, 21, 21, 43, 43, 43, 5, 1, 1, 1, 1, 8, 22, 22, 34, 34, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 44, 11, 12, 13, 14, 15, 43, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 254 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113387 none O=C(CC1=CSC2=NC=CN12)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 8, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 73, 133, 133, 133, 133, 133, 133, 133, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 73, 73, 133, 133, 133, 19, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [38, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 399 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113387 none O=C(CC1=CSC2=NC=CN12)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 8, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 43, 43, 43, 133, 133, 133, 174, 201, 201, 201, 201, 201, 133, 133, 43, 5, 5, 1, 1, 1, 23, 43, 43, 43, 43, 133, 174, 174, 201, 201, 43, 43] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 636 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113387 none O=C(CC1=CSC2=NC=CN12)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 8, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 119, 201, 201, 201, 201, 201, 201, 201, 34, 34, 34, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 34, 119, 119, 201, 201, 201, 52, 34, 34, 34, 34, 7, 4, 4, 2, 2, 34, 34] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 600 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113387 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113387/1 /scratch/stefan/7770410/working/building/REAL300020113387 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 374) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/374 `/scratch/stefan/7770410/working/3D/374' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CSC2=NC=CN12)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113387.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113387 none O=C(CC1=CSC2=NC=CN12)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 8, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 21, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 1, 8, 8, 8, 22, 34, 34, 34, 34, 34, 8, 8, 1, 21, 21, 44, 44, 44, 5, 1, 1, 1, 1, 8, 22, 22, 34, 34, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 44, 11, 12, 13, 14, 15, 43, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 256 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113387 none O=C(CC1=CSC2=NC=CN12)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 8, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 73, 133, 133, 133, 133, 133, 133, 133, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 73, 73, 133, 133, 133, 20, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [38, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 398 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113387 none O=C(CC1=CSC2=NC=CN12)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 8, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 44, 44, 44, 133, 133, 133, 174, 201, 201, 201, 201, 201, 133, 133, 44, 5, 5, 1, 1, 1, 23, 44, 44, 44, 44, 133, 174, 174, 201, 201, 44, 44] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 637 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113387 none O=C(CC1=CSC2=NC=CN12)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 8, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 119, 201, 201, 201, 201, 201, 201, 201, 35, 35, 35, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 35, 119, 119, 201, 201, 201, 53, 35, 35, 35, 35, 8, 4, 4, 2, 2, 35, 35] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 596 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113387 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113387 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113387/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113387/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113387 Building REAL300020113388 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113388' /scratch/stefan/7770410/working/building/REAL300020113388 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113388 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113388/0 /scratch/stefan/7770410/working/building/REAL300020113388 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/375 `/scratch/stefan/7770410/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CN1) `REAL300020113388.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113388 none NC(=O)C1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CN1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 36, 51, 59, 59, 59, 59, 11, 11, 1, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 11, 36, 36, 51, 51, 1, 1, 15, 15] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 40, 41, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 42, 43]) total number of confs: 243 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113388 none NC(=O)C1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CN1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 73, 73, 27, 27, 27, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 73, 73, 73, 73, 73, 27, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 73, 73] 201 rigid atoms, others: [35, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 177 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113388 none NC(=O)C1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CN1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 73, 73, 73, 141, 201, 201, 201, 201, 201, 73, 73, 15, 1, 1, 2, 2, 1, 5, 15, 15, 15, 15, 73, 141, 141, 201, 201, 15, 15, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 42, 43, 25, 26, 29] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 817 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113388 none NC(=O)C1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CN1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 91, 91, 91, 59, 59, 59, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 59, 201, 201, 201, 201, 201, 91, 59, 59, 59, 59, 12, 6, 6, 4, 4, 59, 59, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 440 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113388 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113388/1 /scratch/stefan/7770410/working/building/REAL300020113388 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 376) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/376 `/scratch/stefan/7770410/working/3D/376' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CN1) `REAL300020113388.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113388 none NC(=O)C1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CN1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 36, 51, 59, 59, 59, 59, 11, 11, 1, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 11, 36, 36, 51, 51, 1, 1, 15, 15] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 40, 41, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 42, 43]) total number of confs: 243 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113388 none NC(=O)C1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CN1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 73, 73, 27, 27, 27, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 73, 73, 73, 73, 73, 27, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 73, 73] 201 rigid atoms, others: [35, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 177 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113388 none NC(=O)C1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CN1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 73, 73, 73, 141, 201, 201, 201, 201, 201, 73, 73, 15, 1, 1, 2, 2, 1, 5, 15, 15, 15, 15, 73, 141, 141, 201, 201, 15, 15, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 42, 43, 25, 26, 29] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 817 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113388 none NC(=O)C1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CN1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 91, 91, 91, 59, 59, 59, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 59, 201, 201, 201, 201, 201, 91, 59, 59, 59, 59, 12, 6, 6, 4, 4, 59, 59, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 440 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113388 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113388 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113388/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113388/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113388 Building REAL300020113389 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113389' /scratch/stefan/7770410/working/building/REAL300020113389 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113389 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113389/0 /scratch/stefan/7770410/working/building/REAL300020113389 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/377 `/scratch/stefan/7770410/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(COC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113389.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113389 none CC(COC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 18, 35, 39, 39, 35, 39, 39, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 22, 34, 34, 34, 34, 34, 7, 7, 1, 15, 15, 15, 15, 18, 18, 39, 39, 35, 39, 39, 6, 1, 1, 1, 1, 7, 22, 22, 34, 34, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 254 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113389 none CC(COC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 23, 56, 61, 107, 114, 114, 107, 114, 114, 23, 23, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 56, 56, 56, 56, 61, 61, 114, 114, 107, 114, 114, 23, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 371 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113389 none CC(COC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 4, 1, 1, 1, 1, 1, 1, 1, 15, 18, 18, 18, 39, 39, 39, 114, 114, 114, 169, 201, 201, 201, 201, 201, 114, 114, 39, 15, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 18, 39, 39, 39, 39, 114, 169, 169, 201, 201, 39, 39] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 39, 35, 36, 38, 37] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 728 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113389 none CC(COC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 71, 128, 133, 201, 201, 201, 201, 201, 201, 71, 71, 36, 36, 36, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 36, 128, 128, 128, 128, 133, 133, 201, 201, 201, 201, 201, 71, 36, 36, 36, 36, 9, 5, 5, 3, 3, 36, 36] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 608 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113389 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113389/1 /scratch/stefan/7770410/working/building/REAL300020113389 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 378) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/378 `/scratch/stefan/7770410/working/3D/378' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(COC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113389.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113389 none CC(COC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 18, 34, 38, 38, 34, 38, 38, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 22, 34, 34, 34, 34, 34, 7, 7, 1, 15, 15, 15, 15, 18, 18, 38, 38, 34, 38, 38, 6, 1, 1, 1, 1, 7, 22, 22, 34, 34, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 252 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113389 none CC(COC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 24, 57, 62, 107, 114, 114, 107, 114, 114, 24, 24, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 57, 57, 57, 57, 62, 62, 114, 114, 107, 114, 114, 24, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 371 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113389 none CC(COC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 4, 1, 1, 1, 1, 1, 1, 1, 15, 18, 18, 18, 38, 38, 38, 114, 114, 114, 168, 201, 201, 201, 201, 201, 114, 114, 38, 15, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 18, 38, 38, 38, 38, 114, 168, 168, 201, 201, 38, 38] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 39, 35, 36, 38, 37] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 725 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113389 none CC(COC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 72, 128, 133, 201, 201, 201, 201, 201, 201, 72, 72, 36, 36, 36, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 36, 128, 128, 128, 128, 133, 133, 201, 201, 201, 201, 201, 72, 36, 36, 36, 36, 9, 5, 5, 3, 3, 36, 36] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 609 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113389 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113389 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113389/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113389/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113389 Building REAL300020113390 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113390' /scratch/stefan/7770410/working/building/REAL300020113390 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113390 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113390/0 /scratch/stefan/7770410/working/building/REAL300020113390 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/379 `/scratch/stefan/7770410/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113390.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113390 none CCN1C=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 27, 27, 27, 27, 27, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 34, 45, 54, 54, 54, 54, 7, 7, 1, 42, 42, 42, 42, 42, 27, 27, 27, 6, 1, 1, 1, 1, 7, 34, 34, 45, 45, 1, 1] 201 rigid atoms, others: [45, 35, 36, 37, 38, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 319 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113390 none CCN1C=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 63, 63, 63, 63, 63, 25, 25, 25, 7, 7, 7, 1, 1, 1, 1, 1, 9, 13, 18, 18, 18, 18, 1, 1, 7, 99, 99, 99, 99, 99, 63, 63, 63, 25, 7, 7, 7, 7, 1, 9, 9, 13, 13, 7, 7] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 392 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113390 none CCN1C=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 27, 27, 27, 63, 63, 63, 126, 143, 144, 144, 144, 144, 63, 63, 27, 4, 4, 4, 4, 4, 1, 1, 1, 9, 27, 27, 27, 27, 63, 126, 126, 143, 143, 27, 27] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 528 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113390 none CCN1C=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 145, 145, 145, 145, 145, 115, 115, 115, 56, 56, 56, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 56, 201, 201, 201, 201, 201, 145, 145, 145, 115, 56, 56, 56, 56, 18, 6, 6, 4, 4, 56, 56] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 706 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113390 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113390/1 /scratch/stefan/7770410/working/building/REAL300020113390 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 380) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/380 `/scratch/stefan/7770410/working/3D/380' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113390.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113390/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113390 none CCN1C=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 26, 26, 26, 26, 26, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 34, 45, 55, 55, 55, 55, 7, 7, 1, 41, 41, 41, 41, 41, 26, 26, 26, 6, 1, 1, 1, 1, 7, 34, 34, 45, 45, 1, 1] 201 rigid atoms, others: [45, 35, 36, 37, 38, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 320 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113390 none CCN1C=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 65, 65, 65, 65, 65, 25, 25, 25, 7, 7, 7, 1, 1, 1, 1, 1, 9, 13, 18, 18, 18, 18, 1, 1, 7, 101, 101, 101, 101, 101, 65, 65, 65, 25, 7, 7, 7, 7, 1, 9, 9, 13, 13, 7, 7] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 396 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113390 none CCN1C=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 26, 26, 26, 65, 65, 65, 126, 142, 143, 143, 143, 143, 65, 65, 26, 4, 4, 4, 4, 4, 1, 1, 1, 9, 26, 26, 26, 26, 65, 126, 126, 142, 142, 26, 26] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 517 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113390 none CCN1C=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 145, 145, 145, 145, 145, 115, 115, 115, 56, 56, 56, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 56, 201, 201, 201, 201, 201, 145, 145, 145, 115, 56, 56, 56, 56, 18, 6, 6, 4, 4, 56, 56] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 706 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113390 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113390 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113390/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113390/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113390 Building REAL300020113391 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113391' /scratch/stefan/7770410/working/building/REAL300020113391 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113391 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113391/0 /scratch/stefan/7770410/working/building/REAL300020113391 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/381 `/scratch/stefan/7770410/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113391.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113391 none CC(C)N1C=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 30, 53, 30, 30, 30, 30, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 34, 46, 59, 59, 59, 59, 7, 7, 1, 53, 53, 53, 53, 53, 53, 53, 30, 30, 30, 6, 1, 1, 1, 1, 7, 34, 34, 46, 46, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 363 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113391 none CC(C)N1C=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 73, 101, 73, 73, 73, 73, 24, 24, 24, 7, 7, 7, 1, 1, 1, 1, 1, 9, 13, 17, 17, 17, 17, 1, 1, 7, 101, 101, 101, 101, 101, 101, 101, 73, 73, 73, 24, 7, 7, 7, 7, 1, 9, 9, 13, 13, 7, 7] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 337 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113391 none CC(C)N1C=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 30, 30, 30, 73, 73, 73, 154, 187, 201, 201, 201, 201, 73, 73, 30, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 10, 30, 30, 30, 30, 73, 154, 154, 187, 187, 30, 30] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 35, 36] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 739 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113391 none CC(C)N1C=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 119, 119, 119, 60, 60, 60, 19, 19, 19, 6, 4, 1, 1, 1, 1, 1, 1, 19, 19, 60, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 119, 60, 60, 60, 60, 19, 6, 6, 4, 4, 60, 60] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 474 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113391 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113391/1 /scratch/stefan/7770410/working/building/REAL300020113391 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 382) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/382 `/scratch/stefan/7770410/working/3D/382' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113391.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113391 none CC(C)N1C=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 29, 52, 29, 29, 29, 29, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 35, 47, 59, 59, 59, 59, 7, 7, 1, 52, 52, 52, 52, 52, 52, 52, 29, 29, 29, 6, 1, 1, 1, 1, 7, 35, 35, 47, 47, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 363 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113391 none CC(C)N1C=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 74, 101, 74, 74, 74, 74, 24, 24, 24, 7, 7, 7, 1, 1, 1, 1, 1, 9, 13, 17, 17, 17, 17, 1, 1, 7, 101, 101, 101, 101, 101, 101, 101, 74, 74, 74, 24, 7, 7, 7, 7, 1, 9, 9, 13, 13, 7, 7] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 335 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113391 none CC(C)N1C=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 29, 29, 29, 74, 74, 74, 157, 189, 201, 201, 201, 201, 74, 74, 29, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 10, 29, 29, 29, 29, 74, 157, 157, 189, 189, 29, 29] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 35, 36] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 740 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113391 none CC(C)N1C=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 118, 118, 118, 59, 59, 59, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 59, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 118, 59, 59, 59, 59, 18, 6, 6, 4, 4, 59, 59] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 474 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113391 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113391 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113391/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113391/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113391 Building REAL300020113392 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113392' /scratch/stefan/7770410/working/building/REAL300020113392 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113392 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113392/0 /scratch/stefan/7770410/working/building/REAL300020113392 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/383 `/scratch/stefan/7770410/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1C(C)(C)C) `REAL300020113392.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113392 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 64, 84, 111, 111, 111, 111, 13, 13, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 13, 64, 64, 84, 84, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 43, 44, 22] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 398 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113392 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 48, 48, 48, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 21, 21, 21, 21, 1, 1, 13, 79, 79, 79, 79, 79, 79, 79, 79, 79, 79, 48, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 79, 79, 79, 79, 79, 79, 79, 79, 79] 201 rigid atoms, others: [38, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 245 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113392 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 79, 79, 79, 164, 201, 201, 201, 201, 201, 79, 79, 13, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 4, 13, 13, 13, 13, 79, 164, 164, 201, 201, 13, 13, 2, 2, 2, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 32, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 749 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113392 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 112, 112, 112, 25, 25, 25, 6, 4, 1, 1, 1, 1, 1, 1, 25, 25, 112, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 112, 112, 112, 112, 25, 6, 6, 4, 4, 112, 112, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 549 number of broken/clashed sets: 201 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113392 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113392/1 /scratch/stefan/7770410/working/building/REAL300020113392 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 384) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/384 `/scratch/stefan/7770410/working/3D/384' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1C(C)(C)C) `REAL300020113392.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113392 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 64, 84, 111, 111, 111, 111, 13, 13, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 13, 64, 64, 84, 84, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 43, 44, 22] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 398 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113392 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 48, 48, 48, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 21, 21, 21, 21, 1, 1, 13, 79, 79, 79, 79, 79, 79, 79, 79, 79, 79, 48, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 79, 79, 79, 79, 79, 79, 79, 79, 79] 201 rigid atoms, others: [38, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 245 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113392 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 79, 79, 79, 164, 201, 201, 201, 201, 201, 79, 79, 13, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 4, 13, 13, 13, 13, 79, 164, 164, 201, 201, 13, 13, 2, 2, 2, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 32, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 749 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113392 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 112, 112, 112, 24, 24, 24, 6, 4, 1, 1, 1, 1, 1, 1, 24, 24, 112, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 112, 112, 112, 112, 24, 6, 6, 4, 4, 112, 112, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 550 number of broken/clashed sets: 201 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113392 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113392 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113392/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113392/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113392 Building REAL300020113393 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113393' /scratch/stefan/7770410/working/building/REAL300020113393 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113393 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113393/0 /scratch/stefan/7770410/working/building/REAL300020113393 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/385 `/scratch/stefan/7770410/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(Cl)N=CS1) `REAL300020113393.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113393 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(Cl)N=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 16, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 22, 67, 67, 67, 67, 67, 22, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9, 67] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 157 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113393 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(Cl)N=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 16, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 46, 46, 46, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 46, 74, 201, 201, 201, 201, 201, 74, 46, 46, 46, 46, 12, 6, 6, 4, 4, 46, 46, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 396 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113393 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(Cl)N=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 16, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 28, 41, 44, 44, 44, 44, 9, 9, 1, 6, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 9, 28, 28, 41, 41, 1, 1, 15] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 35, 36, 26, 27, 28, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 37]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113393 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(Cl)N=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 16, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 15, 15, 15, 67, 67, 67, 145, 201, 201, 201, 201, 201, 67, 67, 15, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 15, 67, 145, 145, 201, 201, 15, 15, 1] 201 rigid atoms, others: [1, 37, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 821 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113393 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113393/1 /scratch/stefan/7770410/working/building/REAL300020113393 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 386) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/386 `/scratch/stefan/7770410/working/3D/386' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(Cl)N=CS1) `REAL300020113393.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113393/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113393 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(Cl)N=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 16, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 23, 68, 68, 68, 68, 68, 23, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9, 68] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 161 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113393 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(Cl)N=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 16, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 47, 47, 47, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 47, 75, 201, 201, 201, 201, 201, 75, 47, 47, 47, 47, 12, 6, 6, 4, 4, 47, 47, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 399 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113393 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(Cl)N=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 16, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 28, 42, 45, 45, 45, 45, 9, 9, 1, 6, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 9, 28, 28, 42, 42, 1, 1, 15] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 35, 36, 26, 27, 28, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 37]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113393 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(Cl)N=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 16, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 15, 15, 15, 68, 68, 68, 146, 201, 201, 201, 201, 201, 68, 68, 15, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 15, 68, 146, 146, 201, 201, 15, 15, 1] 201 rigid atoms, others: [1, 37, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 816 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113393 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113393 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113393/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113393/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113393 Building REAL300020113394 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113394' /scratch/stefan/7770410/working/building/REAL300020113394 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113394 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113394/0 /scratch/stefan/7770410/working/building/REAL300020113394 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/387 `/scratch/stefan/7770410/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(Cl)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113394.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113394 none CCN1C=C(Cl)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 28, 28, 28, 28, 28, 28, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 33, 44, 50, 50, 50, 50, 7, 7, 1, 44, 44, 44, 44, 44, 28, 28, 6, 1, 1, 1, 1, 7, 33, 33, 44, 44, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 44, 10, 11, 12, 13, 14, 45, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 317 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113394 none CCN1C=C(Cl)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 60, 60, 60, 60, 60, 60, 25, 25, 25, 7, 7, 7, 1, 1, 1, 1, 1, 9, 13, 15, 15, 15, 15, 1, 1, 7, 94, 94, 94, 94, 94, 60, 60, 25, 7, 7, 7, 7, 1, 9, 9, 13, 13, 7, 7] 201 rigid atoms, others: [39, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 372 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113394 none CCN1C=C(Cl)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 28, 28, 28, 60, 60, 60, 117, 134, 138, 138, 138, 138, 60, 60, 28, 5, 5, 5, 5, 5, 1, 1, 9, 28, 28, 28, 28, 60, 117, 117, 134, 134, 28, 28] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 33] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 518 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113394 none CCN1C=C(Cl)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 139, 139, 139, 139, 139, 139, 103, 103, 103, 50, 50, 50, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 50, 201, 201, 201, 201, 201, 139, 139, 103, 50, 50, 50, 50, 15, 6, 6, 4, 4, 50, 50] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 725 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113394 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113394/1 /scratch/stefan/7770410/working/building/REAL300020113394 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 388) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/388 `/scratch/stefan/7770410/working/3D/388' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(Cl)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113394.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113394/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113394 none CCN1C=C(Cl)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 27, 27, 27, 27, 27, 27, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 33, 44, 51, 51, 51, 51, 7, 7, 1, 44, 44, 44, 44, 44, 27, 27, 6, 1, 1, 1, 1, 7, 33, 33, 44, 44, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 44, 10, 11, 12, 13, 14, 45, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 324 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113394 none CCN1C=C(Cl)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 60, 60, 60, 60, 60, 60, 25, 25, 25, 7, 7, 7, 1, 1, 1, 1, 1, 9, 13, 16, 16, 16, 16, 1, 1, 7, 94, 94, 94, 94, 94, 60, 60, 25, 7, 7, 7, 7, 1, 9, 9, 13, 13, 7, 7] 201 rigid atoms, others: [39, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 374 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113394 none CCN1C=C(Cl)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 27, 27, 27, 60, 60, 60, 118, 134, 138, 138, 138, 138, 60, 60, 27, 5, 5, 5, 5, 5, 1, 1, 9, 27, 27, 27, 27, 60, 118, 118, 134, 134, 27, 27] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 33] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 512 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113394 none CCN1C=C(Cl)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 139, 139, 139, 139, 139, 139, 103, 103, 103, 50, 50, 50, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 50, 201, 201, 201, 201, 201, 139, 139, 103, 50, 50, 50, 50, 15, 6, 6, 4, 4, 50, 50] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 725 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113394 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113394 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113394/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113394/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113394 Building REAL300020113395 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113395' /scratch/stefan/7770410/working/building/REAL300020113395 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113395 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113395/0 /scratch/stefan/7770410/working/building/REAL300020113395 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/389 `/scratch/stefan/7770410/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC=NC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113395.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113395 none CCC1=NC=NC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 23, 23, 23, 10, 23, 23, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 24, 37, 37, 37, 37, 37, 8, 8, 1, 34, 34, 34, 34, 34, 11, 23, 6, 1, 1, 1, 1, 8, 24, 24, 37, 37, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 44, 10, 11, 12, 13, 14, 45, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 271 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113395 none CCC1=NC=NC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 97, 97, 97, 40, 97, 97, 28, 28, 28, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 114, 114, 114, 114, 114, 48, 97, 28, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [39, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 400 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113395 none CCC1=NC=NC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 23, 23, 23, 97, 97, 97, 157, 201, 201, 201, 201, 201, 97, 97, 23, 4, 4, 4, 4, 4, 1, 1, 9, 23, 23, 23, 23, 97, 157, 157, 201, 201, 23, 23] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 33] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 730 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113395 none CCC1=NC=NC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 115, 201, 201, 70, 70, 70, 37, 37, 37, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 37, 201, 201, 201, 201, 201, 138, 201, 70, 37, 37, 37, 37, 7, 4, 4, 2, 2, 37, 37] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 636 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113395 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113395/1 /scratch/stefan/7770410/working/building/REAL300020113395 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 390) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/390 `/scratch/stefan/7770410/working/3D/390' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC=NC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113395.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113395/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113395 none CCC1=NC=NC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 23, 23, 23, 10, 23, 23, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 24, 37, 37, 37, 37, 37, 8, 8, 1, 34, 34, 34, 34, 34, 11, 23, 6, 1, 1, 1, 1, 8, 24, 24, 37, 37, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 44, 10, 11, 12, 13, 14, 45, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 271 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113395 none CCC1=NC=NC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 97, 97, 97, 40, 97, 97, 28, 28, 28, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 114, 114, 114, 114, 114, 47, 97, 28, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [39, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 398 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113395 none CCC1=NC=NC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 23, 23, 23, 97, 97, 97, 157, 201, 201, 201, 201, 201, 97, 97, 23, 4, 4, 4, 4, 4, 1, 1, 9, 23, 23, 23, 23, 97, 157, 157, 201, 201, 23, 23] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 33] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 730 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113395 none CCC1=NC=NC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 113, 201, 201, 70, 70, 70, 37, 37, 37, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 37, 201, 201, 201, 201, 201, 138, 201, 70, 37, 37, 37, 37, 7, 4, 4, 2, 2, 37, 37] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 635 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113395 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113395 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113395/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113395/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113395 Building REAL300020113396 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113396' /scratch/stefan/7770410/working/building/REAL300020113396 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113396 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113396/0 /scratch/stefan/7770410/working/building/REAL300020113396 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/391 `/scratch/stefan/7770410/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NC=NC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113396.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113396 none CC(C)C1=NC=NC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 34, 48, 50, 50, 50, 50, 11, 11, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 11, 34, 34, 48, 48, 1, 1] 201 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 221 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113396 none CC(C)C1=NC=NC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 101, 101, 101, 101, 101, 27, 27, 27, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 101, 101, 101, 101, 101, 101, 101, 101, 101, 27, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 200 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113396 none CC(C)C1=NC=NC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 19, 19, 101, 101, 101, 168, 201, 201, 201, 201, 201, 101, 101, 19, 2, 2, 2, 2, 2, 2, 2, 1, 1, 7, 19, 19, 19, 19, 101, 168, 168, 201, 201, 19, 19] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 35, 36] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 713 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113396 none CC(C)C1=NC=NC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 97, 97, 97, 53, 53, 53, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 53, 201, 201, 201, 201, 201, 201, 201, 201, 201, 97, 53, 53, 53, 53, 10, 5, 5, 3, 3, 53, 53] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 429 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113396 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113396/1 /scratch/stefan/7770410/working/building/REAL300020113396 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 392) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/392 `/scratch/stefan/7770410/working/3D/392' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NC=NC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113396.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113396/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113396 none CC(C)C1=NC=NC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 34, 48, 50, 50, 50, 50, 11, 11, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 11, 34, 34, 48, 48, 1, 1] 201 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 221 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113396 none CC(C)C1=NC=NC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 101, 101, 101, 101, 101, 27, 27, 27, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 101, 101, 101, 101, 101, 101, 101, 101, 101, 27, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 200 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113396 none CC(C)C1=NC=NC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 19, 19, 101, 101, 101, 168, 201, 201, 201, 201, 201, 101, 101, 19, 2, 2, 2, 2, 2, 2, 2, 1, 1, 7, 19, 19, 19, 19, 101, 168, 168, 201, 201, 19, 19] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 35, 36] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 713 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113396 none CC(C)C1=NC=NC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 95, 95, 95, 51, 51, 51, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 51, 201, 201, 201, 201, 201, 201, 201, 201, 201, 95, 51, 51, 51, 51, 10, 5, 5, 3, 3, 51, 51] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 426 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113396 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113396 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113396/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113396/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113396 Building REAL300020113397 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113397' /scratch/stefan/7770410/working/building/REAL300020113397 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113397 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113397/0 /scratch/stefan/7770410/working/building/REAL300020113397 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/393 `/scratch/stefan/7770410/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCCOC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113397.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113397 none O=C(CC1CCCOC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 12, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 43, 84, 84, 84, 84, 84, 1, 1, 1, 1, 1, 6, 6, 6, 23, 32, 39, 39, 39, 39, 6, 6, 1, 43, 43, 84, 84, 84, 84, 84, 84, 84, 84, 84, 6, 1, 1, 1, 1, 6, 23, 23, 32, 32, 1, 1] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 412 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113397 none O=C(CC1CCCOC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 12, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 91, 125, 125, 125, 125, 125, 6, 6, 6, 1, 1, 1, 1, 1, 7, 9, 13, 13, 13, 13, 1, 1, 6, 91, 91, 125, 125, 125, 125, 125, 125, 125, 125, 125, 22, 6, 6, 6, 6, 1, 7, 7, 9, 9, 6, 6] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 467 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113397 none O=C(CC1CCCOC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 12, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 10, 1, 1, 1, 1, 1, 1, 1, 33, 33, 84, 84, 84, 125, 125, 125, 180, 201, 201, 201, 201, 201, 125, 125, 84, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 84, 84, 84, 84, 125, 180, 180, 201, 201, 84, 84] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 712 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113397 none O=C(CC1CCCOC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 12, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 179, 201, 201, 201, 201, 201, 43, 43, 43, 18, 18, 18, 7, 4, 1, 1, 1, 1, 1, 1, 18, 18, 43, 179, 179, 201, 201, 201, 201, 201, 201, 201, 201, 201, 64, 43, 43, 43, 43, 18, 7, 7, 4, 4, 43, 43] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 723 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113397 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113397/1 /scratch/stefan/7770410/working/building/REAL300020113397 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 394) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/394 `/scratch/stefan/7770410/working/3D/394' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCCOC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113397.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113397/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113397 none O=C(CC1CCCOC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 12, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 43, 84, 84, 84, 84, 84, 1, 1, 1, 1, 1, 6, 6, 6, 23, 32, 39, 39, 39, 39, 6, 6, 1, 43, 43, 84, 84, 84, 84, 84, 84, 84, 84, 84, 6, 1, 1, 1, 1, 6, 23, 23, 32, 32, 1, 1] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 412 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113397 none O=C(CC1CCCOC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 12, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 91, 125, 125, 125, 125, 125, 6, 6, 6, 1, 1, 1, 1, 1, 7, 9, 13, 13, 13, 13, 1, 1, 6, 91, 91, 125, 125, 125, 125, 125, 125, 125, 125, 125, 22, 6, 6, 6, 6, 1, 7, 7, 9, 9, 6, 6] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 467 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113397 none O=C(CC1CCCOC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 12, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 10, 1, 1, 1, 1, 1, 1, 1, 33, 33, 84, 84, 84, 125, 125, 125, 180, 201, 201, 201, 201, 201, 125, 125, 84, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 84, 84, 84, 84, 125, 180, 180, 201, 201, 84, 84] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 712 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113397 none O=C(CC1CCCOC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 12, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 178, 201, 201, 201, 201, 201, 43, 43, 43, 18, 18, 18, 7, 4, 1, 1, 1, 1, 1, 1, 18, 18, 43, 178, 178, 201, 201, 201, 201, 201, 201, 201, 201, 201, 63, 43, 43, 43, 43, 18, 7, 7, 4, 4, 43, 43] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 723 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113397 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113397 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113397/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113397/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113397 Building REAL300020113398 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113398' /scratch/stefan/7770410/working/building/REAL300020113398 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113398 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113398/0 /scratch/stefan/7770410/working/building/REAL300020113398 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/395 `/scratch/stefan/7770410/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC=CCC1) `REAL300020113398.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113398 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC=CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 36, 90, 90, 90, 90, 90, 90, 36, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 90, 90, 90, 90, 90, 90, 90, 90, 90, 90, 90] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 279 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113398 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC=CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 51, 51, 51, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 51, 113, 201, 201, 201, 201, 201, 201, 113, 51, 51, 51, 51, 13, 6, 6, 4, 4, 51, 51, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 587 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113398 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC=CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 32, 46, 50, 50, 50, 50, 11, 11, 1, 6, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 32, 32, 46, 46, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113398 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC=CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 22, 22, 22, 90, 90, 90, 153, 201, 201, 201, 201, 201, 90, 90, 22, 1, 1, 1, 1, 1, 1, 1, 9, 22, 22, 22, 22, 90, 153, 153, 201, 201, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 755 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113398 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113398/1 /scratch/stefan/7770410/working/building/REAL300020113398 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 396) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/396 `/scratch/stefan/7770410/working/3D/396' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC=CCC1) `REAL300020113398.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113398 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC=CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 36, 90, 90, 90, 90, 90, 90, 36, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 90, 90, 90, 90, 90, 90, 90, 90, 90, 90, 90] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 279 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113398 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC=CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 51, 51, 51, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 51, 112, 201, 201, 201, 201, 201, 201, 112, 51, 51, 51, 51, 13, 6, 6, 4, 4, 51, 51, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 587 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113398 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC=CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 32, 46, 50, 50, 50, 50, 11, 11, 1, 6, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 32, 32, 46, 46, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113398 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC=CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 22, 22, 22, 90, 90, 90, 152, 201, 201, 201, 201, 201, 90, 90, 22, 1, 1, 1, 1, 1, 1, 1, 9, 22, 22, 22, 22, 90, 152, 152, 201, 201, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 758 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113398 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113398 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113398/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113398/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113398 Building REAL300020113399 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113399' /scratch/stefan/7770410/working/building/REAL300020113399 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113399 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113399/0 /scratch/stefan/7770410/working/building/REAL300020113399 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/397 `/scratch/stefan/7770410/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020113399.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113399 none NC(=O)C1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 3] 3 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 43, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 10 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113399 none NC(=O)C1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [37, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 16 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113399 none NC(=O)C1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1] 3 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 44, 27, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113399 none NC(=O)C1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 3, 3, 3] 3 rigid atoms, others: [40, 41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 10 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113399 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113399/1 /scratch/stefan/7770410/working/building/REAL300020113399 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 398) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/398 `/scratch/stefan/7770410/working/3D/398' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020113399.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113399 none NC(=O)C1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 3] 3 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 43, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 10 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113399 none NC(=O)C1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [37, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 16 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113399 none NC(=O)C1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1] 3 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 44, 27, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113399 none NC(=O)C1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 3, 3, 3] 3 rigid atoms, others: [40, 41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 10 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113399 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113399 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113399/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113399/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113399 Building REAL300020113400 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113400' /scratch/stefan/7770410/working/building/REAL300020113400 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113400 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113400/0 /scratch/stefan/7770410/working/building/REAL300020113400 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/399 `/scratch/stefan/7770410/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCS(=O)(=O)N1) `REAL300020113400.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113400 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCS(=O)(=O)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 14, 11, 11, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 13, 57, 170, 170, 170, 170, 170, 170, 57, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 170, 170, 170, 170, 170, 170] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 488 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113400 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCS(=O)(=O)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 14, 11, 11, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 40, 40, 40, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 40, 113, 201, 201, 201, 201, 201, 201, 113, 40, 40, 40, 40, 7, 4, 4, 2, 2, 40, 40, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 586 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113400 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCS(=O)(=O)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 14, 11, 11, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 29, 40, 40, 40, 40, 40, 13, 13, 1, 6, 39, 39, 39, 39, 39, 39, 6, 1, 1, 1, 1, 13, 29, 29, 40, 40, 1, 1, 39, 39, 39, 39, 39, 39] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43]) total number of confs: 252 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113400 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCS(=O)(=O)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 14, 11, 11, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 39, 39, 39, 170, 170, 170, 194, 201, 201, 201, 201, 201, 170, 170, 39, 1, 1, 1, 1, 1, 1, 1, 12, 39, 39, 39, 39, 170, 194, 194, 201, 201, 39, 39, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 38, 39, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 438 number of broken/clashed sets: 2 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113400 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113400/1 /scratch/stefan/7770410/working/building/REAL300020113400 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 400) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/400 `/scratch/stefan/7770410/working/3D/400' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCS(=O)(=O)N1) `REAL300020113400.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113400 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCS(=O)(=O)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 14, 11, 11, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 13, 57, 170, 170, 170, 170, 170, 170, 57, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 170, 170, 170, 170, 170, 170] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 488 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113400 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCS(=O)(=O)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 14, 11, 11, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 40, 40, 40, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 40, 112, 201, 201, 201, 201, 201, 201, 112, 40, 40, 40, 40, 7, 4, 4, 2, 2, 40, 40, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 584 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113400 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCS(=O)(=O)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 14, 11, 11, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 29, 40, 40, 40, 40, 40, 13, 13, 1, 6, 39, 39, 39, 39, 39, 39, 6, 1, 1, 1, 1, 13, 29, 29, 40, 40, 1, 1, 39, 39, 39, 39, 39, 39] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43]) total number of confs: 252 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113400 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCS(=O)(=O)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 14, 11, 11, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 39, 39, 39, 170, 170, 170, 194, 201, 201, 201, 201, 201, 170, 170, 39, 1, 1, 1, 1, 1, 1, 1, 12, 39, 39, 39, 39, 170, 194, 194, 201, 201, 39, 39, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 38, 39, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 438 number of broken/clashed sets: 2 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113400 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113400 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113400/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113400/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113400 Building REAL300020113401 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113401' /scratch/stefan/7770410/working/building/REAL300020113401 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113401 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113401/0 /scratch/stefan/7770410/working/building/REAL300020113401 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/401 `/scratch/stefan/7770410/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1) `REAL300020113401.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113401 none CC1=NC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 27, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 31, 44, 44, 44, 44, 44, 13, 13, 1, 27, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 13, 31, 31, 44, 44, 1, 1] 142 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40]) total number of confs: 220 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113401 none CC1=NC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 108, 108, 56, 56, 56, 13, 13, 13, 1, 1, 1, 1, 1, 7, 9, 9, 9, 9, 9, 1, 1, 13, 108, 108, 108, 108, 108, 108, 56, 13, 13, 13, 13, 1, 7, 7, 9, 9, 13, 13] 142 rigid atoms, others: [36, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 253 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113401 none CC1=NC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 27, 27, 27, 108, 108, 108, 134, 142, 142, 142, 142, 142, 108, 108, 27, 1, 2, 2, 2, 1, 1, 12, 27, 27, 27, 27, 108, 134, 134, 142, 142, 27, 27] 142 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 357 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113401 none CC1=NC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [142, 142, 142, 142, 142, 100, 100, 100, 44, 44, 44, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 44, 142, 142, 142, 142, 142, 142, 100, 44, 44, 44, 44, 9, 4, 4, 2, 2, 44, 44] 142 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 353 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113401 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113401/1 /scratch/stefan/7770410/working/building/REAL300020113401 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 402) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/402 `/scratch/stefan/7770410/working/3D/402' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1) `REAL300020113401.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113401 none CC1=NC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 27, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 30, 43, 43, 43, 43, 43, 13, 13, 1, 27, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 13, 30, 30, 43, 43, 1, 1] 141 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40]) total number of confs: 217 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113401 none CC1=NC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 108, 108, 56, 56, 56, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 108, 108, 108, 108, 108, 108, 56, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 141 rigid atoms, others: [36, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 250 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113401 none CC1=NC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 27, 27, 27, 108, 108, 108, 133, 141, 141, 141, 141, 141, 108, 108, 27, 1, 2, 2, 2, 1, 1, 12, 27, 27, 27, 27, 108, 133, 133, 141, 141, 27, 27] 141 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 354 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113401 none CC1=NC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [141, 141, 141, 141, 141, 99, 99, 99, 43, 43, 43, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 43, 141, 141, 141, 141, 141, 141, 99, 43, 43, 43, 43, 8, 4, 4, 2, 2, 43, 43] 141 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 352 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113401 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113401 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113401/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113401/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113401 Building REAL300020113402 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113402' /scratch/stefan/7770410/working/building/REAL300020113402 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113402 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113402/0 /scratch/stefan/7770410/working/building/REAL300020113402 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/403 `/scratch/stefan/7770410/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC(C)=C1F) `REAL300020113402.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113402 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC(C)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 47, 65, 78, 78, 78, 78, 12, 12, 1, 11, 11, 11, 6, 6, 11, 11, 11, 11, 6, 1, 1, 1, 1, 12, 47, 47, 65, 65, 1, 1, 11, 11, 11, 11] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 319 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113402 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC(C)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 39, 39, 39, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 12, 70, 70, 70, 39, 39, 70, 70, 70, 70, 39, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 70, 70, 70, 70] 201 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 303 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113402 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC(C)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 80, 80, 80, 157, 201, 201, 201, 201, 201, 80, 80, 11, 1, 1, 1, 1, 1, 2, 2, 2, 1, 3, 11, 11, 11, 11, 80, 157, 157, 201, 201, 11, 11, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 44, 23, 24, 25, 26, 27, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 772 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113402 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC(C)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 122, 122, 122, 81, 81, 81, 16, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 81, 201, 201, 201, 122, 122, 201, 201, 201, 201, 122, 81, 81, 81, 81, 16, 6, 6, 4, 4, 81, 81, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 745 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113402 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113402/1 /scratch/stefan/7770410/working/building/REAL300020113402 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 404) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/404 `/scratch/stefan/7770410/working/3D/404' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC(C)=C1F) `REAL300020113402.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113402/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113402 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC(C)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 47, 65, 78, 78, 78, 78, 12, 12, 1, 11, 11, 11, 6, 6, 11, 11, 11, 11, 6, 1, 1, 1, 1, 12, 47, 47, 65, 65, 1, 1, 11, 11, 11, 11] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 319 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113402 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC(C)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 39, 39, 39, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 12, 70, 70, 70, 39, 39, 70, 70, 70, 70, 39, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 70, 70, 70, 70] 201 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 303 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113402 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC(C)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 79, 79, 79, 157, 201, 201, 201, 201, 201, 79, 79, 11, 1, 1, 1, 1, 1, 2, 2, 2, 1, 3, 11, 11, 11, 11, 79, 157, 157, 201, 201, 11, 11, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 44, 23, 24, 25, 26, 27, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 774 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113402 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC(C)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 121, 121, 121, 80, 80, 80, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 80, 201, 201, 201, 121, 121, 201, 201, 201, 201, 121, 80, 80, 80, 80, 15, 6, 6, 4, 4, 80, 80, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 749 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113402 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113402 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113402/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113402/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113402 Building REAL300020113403 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113403' /scratch/stefan/7770410/working/building/REAL300020113403 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113403 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113403/0 /scratch/stefan/7770410/working/building/REAL300020113403 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/405 `/scratch/stefan/7770410/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN2C=CC=NC2=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113403.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113403 none CC1=NN2C=CC=NC2=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 65, 83, 101, 101, 101, 101, 13, 13, 1, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 65, 65, 83, 83, 1, 1] 201 rigid atoms, others: [45, 36, 37, 38, 39, 12, 13, 14, 15, 16, 46, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 374 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113403 none CC1=NN2C=CC=NC2=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 87, 87, 87, 87, 87, 87, 54, 54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 18, 18, 18, 18, 1, 1, 13, 87, 87, 87, 87, 87, 87, 54, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13] 201 rigid atoms, others: [40, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 246 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113403 none CC1=NN2C=CC=NC2=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 16, 16, 16, 87, 87, 87, 172, 201, 201, 201, 201, 201, 87, 87, 16, 2, 2, 2, 1, 1, 1, 4, 16, 16, 16, 16, 87, 172, 172, 201, 201, 16, 16] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 10, 7, 34, 33] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 722 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113403 none CC1=NN2C=CC=NC2=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 199, 199, 199, 102, 102, 102, 21, 21, 21, 6, 4, 1, 1, 1, 1, 1, 1, 21, 21, 102, 201, 201, 201, 201, 201, 201, 199, 102, 102, 102, 102, 21, 6, 6, 4, 4, 102, 102] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 547 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113403 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113403/1 /scratch/stefan/7770410/working/building/REAL300020113403 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 406) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/406 `/scratch/stefan/7770410/working/3D/406' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN2C=CC=NC2=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113403.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113403 none CC1=NN2C=CC=NC2=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 65, 84, 101, 101, 101, 101, 13, 13, 1, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 65, 65, 84, 84, 1, 1] 201 rigid atoms, others: [45, 36, 37, 38, 39, 12, 13, 14, 15, 16, 46, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 378 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113403 none CC1=NN2C=CC=NC2=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 87, 87, 87, 87, 87, 87, 54, 54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 9, 12, 19, 19, 19, 19, 1, 1, 13, 87, 87, 87, 87, 87, 87, 54, 13, 13, 13, 13, 1, 9, 9, 12, 12, 13, 13] 201 rigid atoms, others: [40, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 252 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113403 none CC1=NN2C=CC=NC2=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 16, 16, 16, 87, 87, 87, 172, 201, 201, 201, 201, 201, 87, 87, 16, 2, 2, 2, 1, 1, 1, 4, 16, 16, 16, 16, 87, 172, 172, 201, 201, 16, 16] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 10, 7, 34, 33] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 719 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113403 none CC1=NN2C=CC=NC2=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 199, 199, 199, 102, 102, 102, 23, 23, 23, 6, 4, 1, 1, 1, 1, 1, 1, 23, 23, 102, 201, 201, 201, 201, 201, 201, 199, 102, 102, 102, 102, 23, 6, 6, 4, 4, 102, 102] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 542 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113403 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113403 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113403/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113403/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113403 Building REAL300020113404 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113404' /scratch/stefan/7770410/working/building/REAL300020113404 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113404 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113404/0 /scratch/stefan/7770410/working/building/REAL300020113404 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 407) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/407 `/scratch/stefan/7770410/working/3D/407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC[NH+]1CCCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113404.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113404 none O=C(CCC[NH+]1CCCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 10, 10, 10, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 10, 10, 10, 10, 10, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1] 20 rigid atoms, others: [16, 12, 13, 46, 15, 48, 49, 14, 55, 56, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53, 54]) total number of confs: 69 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113404 none O=C(CCC[NH+]1CCCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 20, 20, 20, 20, 20, 20, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 8, 13, 13, 13, 13, 13, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 13, 8, 8, 8, 8, 1, 3, 3, 3, 3, 8, 8] 20 rigid atoms, others: [50, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56]) total number of confs: 68 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113404 none O=C(CCC[NH+]1CCCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 5, 4, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 16, 16, 16, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 16, 7, 7, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 16, 16, 16, 16, 20, 20, 20, 20, 20, 16, 16] 20 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 11, 44, 40, 43, 41, 36, 38, 42, 39, 37] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 70 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113404 none O=C(CCC[NH+]1CCCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 20, 20, 20, 20, 20, 20, 8, 8, 8, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 13, 13, 13, 13, 13, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 13, 8, 8, 8, 8, 3, 3, 3, 1, 1, 8, 8] 20 rigid atoms, others: [22, 19, 20, 21, 54, 23, 24, 25, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 55, 56]) total number of confs: 66 number of broken/clashed sets: 3 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113404 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113404/1 /scratch/stefan/7770410/working/building/REAL300020113404 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 408) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/408 `/scratch/stefan/7770410/working/3D/408' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC[NH+]1CCCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113404.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113404 none O=C(CCC[NH+]1CCCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 10, 10, 10, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 10, 10, 10, 10, 10, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1] 20 rigid atoms, others: [16, 12, 13, 46, 15, 48, 49, 14, 55, 56, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53, 54]) total number of confs: 69 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113404 none O=C(CCC[NH+]1CCCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 20, 20, 20, 20, 20, 20, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 8, 13, 13, 13, 13, 13, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 13, 8, 8, 8, 8, 1, 3, 3, 3, 3, 8, 8] 20 rigid atoms, others: [50, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56]) total number of confs: 68 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113404 none O=C(CCC[NH+]1CCCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 5, 4, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 16, 16, 16, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 16, 7, 7, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 16, 16, 16, 16, 20, 20, 20, 20, 20, 16, 16] 20 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 11, 44, 40, 43, 41, 36, 38, 42, 39, 37] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 70 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113404 none O=C(CCC[NH+]1CCCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 20, 20, 20, 20, 20, 20, 8, 8, 8, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 13, 13, 13, 13, 13, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 13, 8, 8, 8, 8, 3, 3, 3, 1, 1, 8, 8] 20 rigid atoms, others: [22, 19, 20, 21, 54, 23, 24, 25, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 55, 56]) total number of confs: 66 number of broken/clashed sets: 3 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113404 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113404 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113404/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113404/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113404 Building REAL300020113405 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113405' /scratch/stefan/7770410/working/building/REAL300020113405 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113405 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113405/0 /scratch/stefan/7770410/working/building/REAL300020113405 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/409 `/scratch/stefan/7770410/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)NCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113405.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113405 none CCC(C)C(=O)NCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 80, 111, 80, 80, 80, 21, 21, 21, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 111, 111, 111, 111, 111, 111, 111, 111, 111, 80, 80, 80, 21, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [44, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 484 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113405 none CCC(C)C(=O)NCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 156, 201, 156, 156, 156, 59, 59, 59, 35, 35, 35, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 35, 201, 201, 201, 201, 201, 201, 201, 201, 201, 156, 156, 156, 59, 35, 35, 35, 35, 8, 4, 4, 2, 2, 35, 35] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 851 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113405 none CCC(C)C(=O)NCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 26, 40, 26, 26, 24, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 35, 35, 35, 35, 8, 8, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 26, 24, 24, 5, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1] 201 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 49, 50, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 309 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113405 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113405/1 /scratch/stefan/7770410/working/building/REAL300020113405 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 410) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/410 `/scratch/stefan/7770410/working/3D/410' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)NCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113405.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113405 none CCC(C)C(=O)NCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 80, 111, 80, 80, 80, 21, 21, 21, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 111, 111, 111, 111, 111, 111, 111, 111, 111, 80, 80, 80, 21, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [44, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 484 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113405 none CCC(C)C(=O)NCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 156, 201, 156, 156, 156, 59, 59, 59, 35, 35, 35, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 35, 201, 201, 201, 201, 201, 201, 201, 201, 201, 156, 156, 156, 59, 35, 35, 35, 35, 8, 4, 4, 2, 2, 35, 35] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 851 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113405 none CCC(C)C(=O)NCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 26, 40, 26, 26, 24, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 35, 35, 35, 35, 8, 8, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 26, 24, 24, 5, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1] 201 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 49, 50, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 309 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113405 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113405 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113405/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113405/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113405 Building REAL300020113406 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113406' /scratch/stefan/7770410/working/building/REAL300020113406 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113406 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113406/0 /scratch/stefan/7770410/working/building/REAL300020113406 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/411 `/scratch/stefan/7770410/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCN1CCCC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113406.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113406 none O=C(CCN1CCCC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 25, 30, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 36, 36, 36, 36, 8, 8, 1, 25, 25, 30, 30, 34, 34, 34, 34, 34, 34, 6, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 268 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113406 none O=C(CCN1CCCC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 97, 105, 113, 113, 113, 113, 113, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 97, 97, 105, 105, 113, 113, 113, 113, 113, 113, 21, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 429 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113406 none O=C(CCN1CCCC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 8, 6, 1, 1, 1, 1, 1, 1, 1, 19, 19, 34, 34, 34, 113, 113, 113, 170, 201, 201, 201, 201, 201, 113, 113, 34, 8, 8, 6, 6, 1, 1, 1, 1, 1, 1, 19, 34, 34, 34, 34, 113, 170, 170, 201, 201, 34, 34] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 35, 36, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 708 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113406 none O=C(CCN1CCCC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 198, 201, 201, 201, 201, 201, 201, 37, 37, 37, 11, 11, 11, 5, 3, 1, 1, 1, 1, 1, 1, 11, 11, 37, 198, 198, 201, 201, 201, 201, 201, 201, 201, 201, 61, 37, 37, 37, 37, 11, 5, 5, 3, 3, 37, 37] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 730 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113406 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113406/1 /scratch/stefan/7770410/working/building/REAL300020113406 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 412) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/412 `/scratch/stefan/7770410/working/3D/412' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCN1CCCC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113406.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113406/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113406 none O=C(CCN1CCCC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 25, 30, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 36, 36, 36, 36, 8, 8, 1, 25, 25, 30, 30, 34, 34, 34, 34, 34, 34, 6, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 268 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113406 none O=C(CCN1CCCC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 97, 105, 113, 113, 113, 113, 113, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 97, 97, 105, 105, 113, 113, 113, 113, 113, 113, 21, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 429 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113406 none O=C(CCN1CCCC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 8, 6, 1, 1, 1, 1, 1, 1, 1, 19, 19, 34, 34, 34, 113, 113, 113, 170, 201, 201, 201, 201, 201, 113, 113, 34, 8, 8, 6, 6, 1, 1, 1, 1, 1, 1, 19, 34, 34, 34, 34, 113, 170, 170, 201, 201, 34, 34] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 35, 36, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 708 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113406 none O=C(CCN1CCCC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 198, 201, 201, 201, 201, 201, 201, 37, 37, 37, 11, 11, 11, 5, 3, 1, 1, 1, 1, 1, 1, 11, 11, 37, 198, 198, 201, 201, 201, 201, 201, 201, 201, 201, 62, 37, 37, 37, 37, 11, 5, 5, 3, 3, 37, 37] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 731 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113406 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113406 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113406/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113406/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113406 Building REAL300020113407 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113407' /scratch/stefan/7770410/working/building/REAL300020113407 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113407 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113407/0 /scratch/stefan/7770410/working/building/REAL300020113407 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/413 `/scratch/stefan/7770410/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113407.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113407 none CNS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [123, 112, 70, 112, 112, 21, 21, 21, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 123, 123, 123, 123, 70, 70, 21, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [36, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 551 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113407 none CNS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 154, 201, 201, 64, 64, 64, 38, 38, 38, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 38, 201, 201, 201, 201, 154, 154, 64, 38, 38, 38, 38, 10, 6, 6, 4, 4, 38, 38] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 869 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113407 none CNS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 35, 19, 35, 35, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 25, 37, 39, 39, 39, 39, 9, 9, 1, 43, 43, 43, 43, 19, 19, 5, 1, 1, 1, 1, 9, 25, 25, 37, 37, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40]) total number of confs: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113407 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113407/1 /scratch/stefan/7770410/working/building/REAL300020113407 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 414) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/414 `/scratch/stefan/7770410/working/3D/414' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113407.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113407/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113407 none CNS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 113, 71, 113, 113, 21, 21, 21, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 9, 124, 124, 124, 124, 71, 71, 21, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [36, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 552 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113407 none CNS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 153, 201, 201, 64, 64, 64, 38, 38, 38, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 38, 201, 201, 201, 201, 153, 153, 64, 38, 38, 38, 38, 10, 6, 6, 4, 4, 38, 38] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 872 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113407 none CNS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 36, 20, 36, 36, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 25, 37, 38, 38, 38, 38, 9, 9, 1, 44, 44, 44, 44, 20, 20, 5, 1, 1, 1, 1, 9, 25, 25, 37, 37, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40]) total number of confs: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113407 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113407 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113407/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113407/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113407 Building REAL300020113408 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113408' /scratch/stefan/7770410/working/building/REAL300020113408 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113408 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113408/0 /scratch/stefan/7770410/working/building/REAL300020113408 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 415) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/415 `/scratch/stefan/7770410/working/3D/415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113408.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113408 none CCCS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 108, 94, 108, 108, 30, 30, 30, 9, 9, 9, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 9, 115, 115, 115, 115, 115, 115, 115, 94, 94, 30, 9, 9, 9, 9, 1, 5, 5, 7, 7, 9, 9] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 483 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113408 none CCCS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 103, 103, 103, 41, 41, 41, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 41, 201, 201, 201, 201, 201, 201, 201, 201, 201, 103, 41, 41, 41, 41, 7, 4, 4, 2, 2, 41, 41] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 732 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113408 none CCCS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 33, 23, 33, 33, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 26, 40, 40, 40, 40, 40, 9, 9, 1, 39, 39, 39, 39, 39, 39, 39, 23, 23, 6, 1, 1, 1, 1, 9, 26, 26, 40, 40, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 340 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113408 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113408/1 /scratch/stefan/7770410/working/building/REAL300020113408 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 416) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/416 `/scratch/stefan/7770410/working/3D/416' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113408.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113408 none CCCS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 109, 94, 109, 109, 30, 30, 30, 9, 9, 9, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 9, 115, 115, 115, 115, 115, 115, 115, 94, 94, 30, 9, 9, 9, 9, 1, 5, 5, 7, 7, 9, 9] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 483 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113408 none CCCS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 102, 102, 102, 40, 40, 40, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 40, 201, 201, 201, 201, 201, 201, 201, 201, 201, 102, 40, 40, 40, 40, 7, 4, 4, 2, 2, 40, 40] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 734 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113408 none CCCS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 34, 23, 34, 34, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 26, 40, 40, 40, 40, 40, 9, 9, 1, 39, 39, 39, 39, 39, 39, 39, 23, 23, 6, 1, 1, 1, 1, 9, 26, 26, 40, 40, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 340 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113408 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113408 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113408/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113408/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113408 Building REAL300020113409 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113409' /scratch/stefan/7770410/working/building/REAL300020113409 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113409 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113409/0 /scratch/stefan/7770410/working/building/REAL300020113409 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/417 `/scratch/stefan/7770410/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)S(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113409.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113409 none CC(C)S(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 106, 116, 95, 106, 106, 33, 33, 33, 10, 10, 10, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 10, 116, 116, 116, 116, 116, 116, 116, 95, 95, 33, 10, 10, 10, 10, 1, 7, 7, 9, 9, 10, 10] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 507 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113409 none CC(C)S(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 200, 201, 201, 96, 96, 96, 48, 48, 48, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 48, 201, 201, 201, 201, 201, 201, 201, 200, 200, 96, 48, 48, 48, 48, 10, 5, 5, 3, 3, 48, 48] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 763 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113409 none CC(C)S(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 28, 32, 22, 28, 28, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 33, 48, 52, 52, 52, 52, 10, 10, 1, 32, 32, 32, 32, 32, 32, 32, 22, 22, 6, 1, 1, 1, 1, 10, 33, 33, 48, 48, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 334 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113409 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113409/1 /scratch/stefan/7770410/working/building/REAL300020113409 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 418) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/418 `/scratch/stefan/7770410/working/3D/418' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)S(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113409.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113409 none CC(C)S(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 106, 116, 95, 106, 106, 33, 33, 33, 10, 10, 10, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 10, 116, 116, 116, 116, 116, 116, 116, 95, 95, 33, 10, 10, 10, 10, 1, 7, 7, 9, 9, 10, 10] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 507 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113409 none CC(C)S(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 200, 201, 201, 96, 96, 96, 48, 48, 48, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 48, 201, 201, 201, 201, 201, 201, 201, 200, 200, 96, 48, 48, 48, 48, 10, 5, 5, 3, 3, 48, 48] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 763 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113409 none CC(C)S(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 28, 32, 22, 28, 28, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 33, 48, 51, 51, 51, 51, 10, 10, 1, 32, 32, 32, 32, 32, 32, 32, 22, 22, 6, 1, 1, 1, 1, 10, 33, 33, 48, 48, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 332 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113409 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113409 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113409/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113409/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113409 Building REAL300020113410 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113410' /scratch/stefan/7770410/working/building/REAL300020113410 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113410 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113410/0 /scratch/stefan/7770410/working/building/REAL300020113410 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/419 `/scratch/stefan/7770410/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2NC=CC=C12) `REAL300020113410.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113410 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2NC=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 32, 98, 98, 98, 98, 98, 98, 98, 98, 32, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 98, 98, 98, 98, 98] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 198 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113410 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2NC=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 60, 60, 60, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 60, 118, 201, 201, 201, 201, 201, 201, 201, 201, 118, 60, 60, 60, 60, 11, 6, 6, 4, 4, 60, 60, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 456 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113410 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2NC=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 34, 49, 59, 59, 59, 59, 11, 11, 1, 5, 21, 21, 21, 21, 21, 21, 21, 21, 5, 1, 1, 1, 1, 11, 34, 34, 49, 49, 1, 1, 21, 21, 21, 21, 21] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 245 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113410 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2NC=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 21, 21, 21, 98, 98, 98, 159, 201, 201, 201, 201, 201, 98, 98, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 21, 21, 21, 21, 98, 159, 159, 201, 201, 21, 21, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 733 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113410 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113410/1 /scratch/stefan/7770410/working/building/REAL300020113410 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 420) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/420 `/scratch/stefan/7770410/working/3D/420' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2NC=CC=C12) `REAL300020113410.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113410/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113410 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2NC=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 32, 99, 99, 99, 99, 99, 99, 99, 99, 32, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 99, 99, 99, 99, 99] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 199 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113410 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2NC=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 60, 60, 60, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 60, 118, 201, 201, 201, 201, 201, 201, 201, 201, 118, 60, 60, 60, 60, 11, 6, 6, 4, 4, 60, 60, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 455 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113410 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2NC=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 34, 49, 60, 60, 60, 60, 11, 11, 1, 5, 21, 21, 21, 21, 21, 21, 21, 21, 5, 1, 1, 1, 1, 11, 34, 34, 49, 49, 1, 1, 21, 21, 21, 21, 21] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 247 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113410 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2NC=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 21, 21, 21, 99, 99, 99, 159, 201, 201, 201, 201, 201, 99, 99, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 21, 21, 21, 21, 99, 159, 159, 201, 201, 21, 21, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 728 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113410 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113410 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113410/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113410/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113410 Building REAL300020113411 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113411' /scratch/stefan/7770410/working/building/REAL300020113411 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for REAL300020113411 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113411/0 /scratch/stefan/7770410/working/building/REAL300020113411 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/421 `/scratch/stefan/7770410/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2CCCC[N@@H+]2C1) `REAL300020113411.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113411 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2CCCC[N@@H+]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 9, 9, 9, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 9, 33, 44, 44, 44, 44, 44, 44, 44, 44, 44, 33, 9, 9, 9, 9, 1, 4, 4, 4, 4, 9, 9, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44] 46 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 139 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113411 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2CCCC[N@@H+]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 11, 11, 11, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 35, 46, 46, 46, 46, 46, 46, 46, 46, 46, 35, 11, 11, 11, 11, 4, 3, 3, 1, 1, 11, 11, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46] 46 rigid atoms, others: [37, 38, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 138 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113411 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2CCCC[N@@H+]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 11, 11, 11, 11, 11, 11, 9, 9, 1, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 9, 11, 11, 11, 11, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 46 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113411 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2CCCC[N@@H+]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 16, 16, 16, 44, 44, 44, 46, 46, 46, 46, 46, 46, 44, 44, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 16, 16, 16, 16, 44, 46, 46, 46, 46, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 46 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 94 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113411 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113411/1 /scratch/stefan/7770410/working/building/REAL300020113411 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 422) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/422 `/scratch/stefan/7770410/working/3D/422' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2CCCC[N@H+]2C1) `REAL300020113411.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113411/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113411 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2CCCC[N@H+]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 12, 12, 12, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 12, 37, 67, 67, 67, 67, 67, 67, 67, 67, 67, 37, 12, 12, 12, 12, 1, 5, 5, 5, 5, 12, 12, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67] 77 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 218 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113411 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2CCCC[N@H+]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 26, 26, 26, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 26, 56, 77, 77, 77, 77, 77, 77, 77, 77, 77, 56, 26, 26, 26, 26, 5, 3, 3, 1, 1, 26, 26, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77] 77 rigid atoms, others: [37, 38, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 234 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113411 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2CCCC[N@H+]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 26, 26, 26, 26, 26, 26, 12, 12, 1, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 12, 26, 26, 26, 26, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 77 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113411 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2CCCC[N@H+]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 21, 21, 21, 67, 67, 67, 77, 77, 77, 77, 77, 77, 67, 67, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 21, 67, 77, 77, 77, 77, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 77 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 174 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113411 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `2' /scratch/stefan/7770410/working/building/REAL300020113411/2 /scratch/stefan/7770410/working/building/REAL300020113411 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 2 (index: 423) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/423 `/scratch/stefan/7770410/working/3D/423' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2CCCC[N@@H+]2C1) `REAL300020113411.mol2' -> `2.mol2' `temp.mol2' -> `REAL300020113411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113411/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113411 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2CCCC[N@@H+]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 9, 9, 9, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 9, 33, 44, 44, 44, 44, 44, 44, 44, 44, 44, 33, 9, 9, 9, 9, 1, 4, 4, 4, 4, 9, 9, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44] 46 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 139 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113411 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2CCCC[N@@H+]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 11, 11, 11, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 35, 46, 46, 46, 46, 46, 46, 46, 46, 46, 35, 11, 11, 11, 11, 4, 3, 3, 1, 1, 11, 11, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46] 46 rigid atoms, others: [37, 38, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 138 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113411 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2CCCC[N@@H+]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 11, 11, 11, 11, 11, 11, 9, 9, 1, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 9, 11, 11, 11, 11, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 46 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113411 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2CCCC[N@@H+]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 16, 16, 16, 44, 44, 44, 46, 46, 46, 46, 46, 46, 44, 44, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 16, 16, 16, 16, 44, 46, 46, 46, 46, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 46 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 94 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113411 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `3' /scratch/stefan/7770410/working/building/REAL300020113411/3 /scratch/stefan/7770410/working/building/REAL300020113411 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 3 (index: 424) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/424 `/scratch/stefan/7770410/working/3D/424' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2CCCC[N@H+]2C1) `REAL300020113411.mol2' -> `3.mol2' `temp.mol2' -> `REAL300020113411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113411/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113411 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2CCCC[N@H+]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 12, 12, 12, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 12, 37, 67, 67, 67, 67, 67, 67, 67, 67, 67, 37, 12, 12, 12, 12, 1, 5, 5, 5, 5, 12, 12, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67] 77 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 218 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113411 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2CCCC[N@H+]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 26, 26, 26, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 26, 56, 77, 77, 77, 77, 77, 77, 77, 77, 77, 56, 26, 26, 26, 26, 5, 3, 3, 1, 1, 26, 26, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77] 77 rigid atoms, others: [37, 38, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 234 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113411 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2CCCC[N@H+]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 26, 26, 26, 26, 26, 26, 12, 12, 1, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 12, 26, 26, 26, 26, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 77 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113411 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2CCCC[N@H+]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 21, 21, 21, 67, 67, 67, 77, 77, 77, 77, 77, 77, 67, 67, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 21, 67, 77, 77, 77, 77, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 77 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 174 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113411 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113411 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 2: /scratch/stefan/7770410/working/building/REAL300020113411/2.* 1: /scratch/stefan/7770410/working/building/REAL300020113411/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113411/0.* 3: /scratch/stefan/7770410/working/building/REAL300020113411/3.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113411 Building REAL300020113412 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113412' /scratch/stefan/7770410/working/building/REAL300020113412 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113412 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113412/0 /scratch/stefan/7770410/working/building/REAL300020113412 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/425 `/scratch/stefan/7770410/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N1) `REAL300020113412.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113412 none CC(C)CC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 25, 27, 12, 12, 12, 12, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 31, 46, 50, 50, 50, 50, 10, 10, 1, 12, 27, 27, 27, 27, 27, 27, 27, 25, 25, 12, 6, 1, 1, 1, 1, 10, 31, 31, 46, 46, 1, 1, 12] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50]) total number of confs: 287 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113412 none CC(C)CC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 94, 95, 49, 49, 49, 49, 35, 35, 35, 10, 10, 10, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 10, 49, 95, 95, 95, 95, 95, 95, 95, 94, 94, 49, 35, 10, 10, 10, 10, 1, 7, 7, 9, 9, 10, 10, 49] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 360 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113412 none CC(C)CC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 5, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 49, 49, 49, 104, 133, 138, 138, 138, 138, 49, 49, 12, 1, 6, 6, 6, 6, 6, 6, 6, 5, 5, 1, 4, 12, 12, 12, 12, 49, 104, 104, 133, 133, 12, 12, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 50, 27, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 543 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113412 none CC(C)CC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 138, 138, 138, 138, 121, 121, 121, 49, 49, 49, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 49, 138, 201, 201, 201, 201, 201, 201, 201, 201, 201, 138, 121, 49, 49, 49, 49, 11, 6, 6, 4, 4, 49, 49, 138] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 740 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113412 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113412/1 /scratch/stefan/7770410/working/building/REAL300020113412 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 426) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/426 `/scratch/stefan/7770410/working/3D/426' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N1) `REAL300020113412.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113412 none CC(C)CC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 25, 27, 12, 12, 12, 12, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 30, 45, 49, 49, 49, 49, 10, 10, 1, 12, 27, 27, 27, 27, 27, 27, 27, 25, 25, 12, 6, 1, 1, 1, 1, 10, 30, 30, 45, 45, 1, 1, 12] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50]) total number of confs: 284 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113412 none CC(C)CC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 94, 95, 49, 49, 49, 49, 35, 35, 35, 10, 10, 10, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 10, 49, 95, 95, 95, 95, 95, 95, 95, 94, 94, 49, 35, 10, 10, 10, 10, 1, 7, 7, 9, 9, 10, 10, 49] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 360 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113412 none CC(C)CC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 5, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 49, 49, 49, 103, 133, 138, 138, 138, 138, 49, 49, 12, 1, 6, 6, 6, 6, 6, 6, 6, 5, 5, 1, 4, 12, 12, 12, 12, 49, 103, 103, 133, 133, 12, 12, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 50, 27, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 546 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113412 none CC(C)CC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 137, 137, 137, 137, 120, 120, 120, 49, 49, 49, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 49, 137, 201, 201, 201, 201, 201, 201, 201, 201, 201, 137, 120, 49, 49, 49, 49, 11, 6, 6, 4, 4, 49, 49, 137] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 744 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113412 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113412 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113412/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113412/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113412 Building REAL300020113413 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113413' /scratch/stefan/7770410/working/building/REAL300020113413 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113413 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113413/0 /scratch/stefan/7770410/working/building/REAL300020113413 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/427 `/scratch/stefan/7770410/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CN=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1) `REAL300020113413.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113413 none CN(C)C1=CN=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 8, 16, 8, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 50, 70, 83, 83, 83, 83, 13, 13, 1, 8, 8, 16, 16, 16, 16, 16, 16, 8, 6, 1, 1, 1, 1, 13, 50, 50, 70, 70, 1, 1, 8] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47]) total number of confs: 343 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113413 none CN(C)C1=CN=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 59, 100, 59, 59, 59, 54, 54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 13, 59, 59, 100, 100, 100, 100, 100, 100, 59, 54, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13, 59] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 341 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113413 none CN(C)C1=CN=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 59, 59, 59, 146, 188, 201, 201, 201, 201, 59, 59, 8, 1, 1, 5, 5, 5, 5, 5, 5, 1, 3, 8, 8, 8, 8, 59, 146, 146, 188, 188, 8, 8, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 47, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 749 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113413 none CN(C)C1=CN=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 198, 198, 198, 83, 83, 83, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 83, 201, 201, 201, 201, 201, 201, 201, 201, 201, 198, 83, 83, 83, 83, 12, 6, 6, 4, 4, 83, 83, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 558 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113413 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113413/1 /scratch/stefan/7770410/working/building/REAL300020113413 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 428) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/428 `/scratch/stefan/7770410/working/3D/428' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CN=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1) `REAL300020113413.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113413/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113413 none CN(C)C1=CN=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 8, 16, 8, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 50, 70, 83, 83, 83, 83, 13, 13, 1, 8, 8, 16, 16, 16, 16, 16, 16, 8, 6, 1, 1, 1, 1, 13, 50, 50, 70, 70, 1, 1, 8] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47]) total number of confs: 343 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113413 none CN(C)C1=CN=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 60, 100, 60, 60, 60, 54, 54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 13, 60, 60, 100, 100, 100, 100, 100, 100, 60, 54, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13, 60] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 339 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113413 none CN(C)C1=CN=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 60, 60, 60, 145, 187, 201, 201, 201, 201, 60, 60, 8, 1, 1, 5, 5, 5, 5, 5, 5, 1, 3, 8, 8, 8, 8, 60, 145, 145, 187, 187, 8, 8, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 47, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 743 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113413 none CN(C)C1=CN=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 198, 198, 198, 83, 83, 83, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 83, 201, 201, 201, 201, 201, 201, 201, 201, 201, 198, 83, 83, 83, 83, 12, 6, 6, 4, 4, 83, 83, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 558 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113413 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113413 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113413/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113413/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113413 Building REAL300020113414 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113414' /scratch/stefan/7770410/working/building/REAL300020113414 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113414 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113414/0 /scratch/stefan/7770410/working/building/REAL300020113414 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/429 `/scratch/stefan/7770410/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1) `REAL300020113414.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113414 none CC(C)OC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 14, 23, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 39, 58, 71, 71, 71, 71, 13, 13, 1, 6, 6, 23, 23, 23, 23, 23, 23, 23, 6, 6, 1, 1, 1, 1, 13, 39, 39, 58, 58, 1, 1, 6] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49]) total number of confs: 338 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113414 none CC(C)OC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 72, 110, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 50, 50, 110, 110, 110, 110, 110, 110, 110, 50, 50, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 50] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 430 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113414 none CC(C)OC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 124, 176, 194, 194, 194, 194, 50, 50, 6, 1, 1, 8, 8, 8, 8, 8, 8, 8, 1, 1, 6, 6, 6, 6, 50, 124, 124, 176, 176, 6, 6, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 49, 36, 27, 28, 37] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 768 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113414 none CC(C)OC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 201, 194, 194, 194, 194, 194, 194, 194, 71, 71, 71, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 71, 194, 194, 201, 201, 201, 201, 201, 201, 201, 194, 194, 71, 71, 71, 71, 10, 6, 6, 4, 4, 71, 71, 194] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 541 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113414 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113414/1 /scratch/stefan/7770410/working/building/REAL300020113414 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 430) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/430 `/scratch/stefan/7770410/working/3D/430' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1) `REAL300020113414.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113414/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113414 none CC(C)OC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 14, 23, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 39, 58, 71, 71, 71, 71, 13, 13, 1, 6, 6, 23, 23, 23, 23, 23, 23, 23, 6, 6, 1, 1, 1, 1, 13, 39, 39, 58, 58, 1, 1, 6] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49]) total number of confs: 338 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113414 none CC(C)OC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 72, 110, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 50, 50, 110, 110, 110, 110, 110, 110, 110, 50, 50, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 50] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 430 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113414 none CC(C)OC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 124, 176, 194, 194, 194, 194, 50, 50, 6, 1, 1, 8, 8, 8, 8, 8, 8, 8, 1, 1, 6, 6, 6, 6, 50, 124, 124, 176, 176, 6, 6, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 49, 36, 27, 28, 37] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 768 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113414 none CC(C)OC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 201, 194, 194, 194, 194, 194, 194, 194, 71, 71, 71, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 71, 194, 194, 201, 201, 201, 201, 201, 201, 201, 194, 194, 71, 71, 71, 71, 10, 6, 6, 4, 4, 71, 71, 194] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 541 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113414 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113414 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113414/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113414/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113414 Building REAL300020113415 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113415' /scratch/stefan/7770410/working/building/REAL300020113415 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113415 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113415/0 /scratch/stefan/7770410/working/building/REAL300020113415 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/431 `/scratch/stefan/7770410/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=C2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=CN12) `REAL300020113415.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113415 none CC1=CN=C2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 28, 43, 48, 48, 48, 48, 9, 9, 1, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 9, 28, 28, 43, 43, 1, 1, 17, 17] 201 rigid atoms, others: [45, 35, 36, 37, 38, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47]) total number of confs: 219 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113415 none CC1=CN=C2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 73, 73, 73, 29, 29, 29, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 73, 73, 73, 73, 73, 73, 73, 73, 29, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9, 73, 73] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 176 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113415 none CC1=CN=C2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 73, 73, 73, 141, 201, 201, 201, 201, 201, 73, 73, 17, 1, 1, 1, 2, 2, 2, 1, 1, 5, 17, 17, 17, 17, 73, 141, 141, 201, 201, 17, 17, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 46, 47, 33, 27, 28, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 836 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113415 none CC1=CN=C2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 81, 81, 81, 48, 48, 48, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 48, 201, 201, 201, 201, 201, 201, 201, 201, 81, 48, 48, 48, 48, 11, 6, 6, 4, 4, 48, 48, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 418 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113415 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113415/1 /scratch/stefan/7770410/working/building/REAL300020113415 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 432) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/432 `/scratch/stefan/7770410/working/3D/432' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=C2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=CN12) `REAL300020113415.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113415/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113415 none CC1=CN=C2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 28, 43, 48, 48, 48, 48, 9, 9, 1, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 9, 28, 28, 43, 43, 1, 1, 17, 17] 201 rigid atoms, others: [45, 35, 36, 37, 38, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47]) total number of confs: 219 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113415 none CC1=CN=C2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 73, 73, 73, 29, 29, 29, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 73, 73, 73, 73, 73, 73, 73, 73, 29, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9, 73, 73] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 176 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113415 none CC1=CN=C2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 73, 73, 73, 141, 201, 201, 201, 201, 201, 73, 73, 17, 1, 1, 1, 2, 2, 2, 1, 1, 5, 17, 17, 17, 17, 73, 141, 141, 201, 201, 17, 17, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 46, 47, 33, 27, 28, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 836 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113415 none CC1=CN=C2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 83, 83, 83, 49, 49, 49, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 49, 201, 201, 201, 201, 201, 201, 201, 201, 83, 49, 49, 49, 49, 11, 6, 6, 4, 4, 49, 49, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 422 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113415 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113415 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113415/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113415/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113415 Building REAL300020113416 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113416' /scratch/stefan/7770410/working/building/REAL300020113416 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113416 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113416/0 /scratch/stefan/7770410/working/building/REAL300020113416 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/433 `/scratch/stefan/7770410/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1CC(F)F) `REAL300020113416.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113416 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1CC(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 5, 5, 5, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 5, 19, 57, 57, 57, 57, 57, 106, 107, 107, 19, 5, 5, 5, 5, 1, 5, 5, 7, 7, 5, 5, 57, 57, 106, 106, 107] 145 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 379 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113416 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1CC(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 18, 18, 18, 8, 8, 8, 5, 2, 1, 1, 1, 1, 1, 1, 8, 8, 18, 28, 68, 68, 68, 68, 68, 120, 120, 120, 28, 18, 18, 18, 18, 8, 5, 5, 2, 2, 18, 18, 68, 68, 120, 120, 120] 120 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 420 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113416 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1CC(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 11, 18, 18, 18, 18, 18, 5, 5, 1, 6, 28, 28, 28, 28, 28, 65, 78, 78, 6, 1, 1, 1, 1, 5, 11, 11, 18, 18, 1, 1, 28, 28, 65, 65, 78] 145 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 369 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113416 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1CC(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 28, 28, 28, 57, 57, 57, 72, 84, 84, 84, 84, 84, 57, 57, 28, 1, 1, 1, 1, 1, 1, 6, 16, 16, 9, 28, 28, 28, 28, 57, 72, 72, 84, 84, 28, 28, 1, 1, 6, 6, 16] 145 rigid atoms, others: [1, 40, 41, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 325 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113416 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113416/1 /scratch/stefan/7770410/working/building/REAL300020113416 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 434) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/434 `/scratch/stefan/7770410/working/3D/434' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1CC(F)F) `REAL300020113416.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113416 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1CC(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 5, 5, 5, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 5, 18, 56, 56, 56, 56, 56, 105, 106, 106, 18, 5, 5, 5, 5, 1, 5, 5, 7, 7, 5, 5, 56, 56, 105, 105, 106] 144 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 377 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113416 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1CC(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 18, 18, 18, 8, 8, 8, 5, 2, 1, 1, 1, 1, 1, 1, 8, 8, 18, 28, 69, 69, 69, 69, 69, 121, 121, 121, 28, 18, 18, 18, 18, 8, 5, 5, 2, 2, 18, 18, 69, 69, 121, 121, 121] 121 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 422 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113416 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1CC(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 11, 18, 18, 18, 18, 18, 5, 5, 1, 6, 28, 28, 28, 28, 28, 65, 78, 78, 6, 1, 1, 1, 1, 5, 11, 11, 18, 18, 1, 1, 28, 28, 65, 65, 78] 144 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 369 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113416 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1CC(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 28, 28, 28, 56, 56, 56, 71, 83, 83, 83, 83, 83, 56, 56, 28, 1, 1, 1, 1, 1, 1, 6, 16, 16, 9, 28, 28, 28, 28, 56, 71, 71, 83, 83, 28, 28, 1, 1, 6, 6, 16] 144 rigid atoms, others: [1, 40, 41, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 324 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113416 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113416 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113416/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113416/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113416 Building REAL300020113417 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113417' /scratch/stefan/7770410/working/building/REAL300020113417 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300020113417 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113417/0 /scratch/stefan/7770410/working/building/REAL300020113417 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/435 `/scratch/stefan/7770410/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[NH+]1CCCCC1) `REAL300020113417.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113417 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[NH+]1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [103, 31, 103, 31, 31, 10, 10, 10, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 10, 103, 123, 123, 123, 123, 123, 123, 103, 103, 103, 103, 103, 103, 31, 10, 10, 10, 10, 1, 3, 3, 3, 3, 10, 10, 123, 123, 123, 123, 123, 123, 123, 123, 123, 123] 123 rigid atoms, others: [8, 9, 10, 11, 12, 40, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 453 number of broken/clashed sets: 110 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113417 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[NH+]1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [81, 28, 81, 28, 28, 9, 9, 9, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 81, 93, 93, 93, 93, 93, 93, 81, 81, 81, 81, 81, 81, 28, 9, 9, 9, 9, 4, 3, 3, 1, 1, 9, 9, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93] 93 rigid atoms, others: [12, 43, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 337 number of broken/clashed sets: 86 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113417 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[NH+]1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [36, 6, 36, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 36, 52, 52, 52, 52, 52, 52, 36, 36, 36, 36, 36, 36, 6, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52] 123 rigid atoms, others: [36, 5, 6, 7, 8, 9, 39, 45, 46, 21, 38, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 186 number of broken/clashed sets: 110 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113417 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[NH+]1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 20, 20, 20, 52, 52, 52, 123, 123, 123, 123, 123, 123, 123, 123, 123, 123, 123, 52, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 9, 9, 9, 20, 52, 52, 52, 52, 123, 123, 123, 123, 123, 52, 52, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 123 rigid atoms, others: [1, 56, 54, 55, 47, 48, 49, 50, 51, 52, 53, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 265 number of broken/clashed sets: 110 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113417 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113417 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 0: /scratch/stefan/7770410/working/building/REAL300020113417/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113417 Building REAL300020113418 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113418' /scratch/stefan/7770410/working/building/REAL300020113418 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for REAL300020113418 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113418/0 /scratch/stefan/7770410/working/building/REAL300020113418 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/436 `/scratch/stefan/7770410/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=C2CCCCC2=NN1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113418.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113418 none O=C(CC1=C2CCCCC2=NN1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 5, 5, 5, 5, 1, 8, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 24, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 10, 10, 10, 28, 41, 41, 41, 41, 41, 10, 10, 1, 24, 24, 32, 32, 32, 32, 32, 32, 32, 32, 32, 6, 1, 1, 1, 1, 10, 28, 28, 41, 41, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 259 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113418 none O=C(CC1=C2CCCCC2=NN1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 5, 5, 5, 5, 1, 8, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 89, 121, 121, 121, 121, 121, 121, 121, 115, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 10, 89, 89, 121, 121, 121, 121, 121, 121, 121, 121, 121, 27, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 417 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113418 none O=C(CC1=C2CCCCC2=NN1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 5, 5, 5, 5, 1, 8, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 32, 32, 32, 121, 121, 121, 169, 201, 201, 201, 201, 201, 121, 121, 32, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 32, 32, 32, 32, 121, 169, 169, 201, 201, 32, 32] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 36, 38, 37, 39, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 666 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113418 none O=C(CC1=C2CCCCC2=NN1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 5, 5, 5, 5, 1, 8, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 167, 201, 201, 201, 201, 201, 201, 201, 192, 41, 41, 41, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 41, 167, 167, 201, 201, 201, 201, 201, 201, 201, 201, 201, 82, 41, 41, 41, 41, 9, 4, 4, 2, 2, 41, 41] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 693 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113418 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113418/1 /scratch/stefan/7770410/working/building/REAL300020113418 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 437) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/437 `/scratch/stefan/7770410/working/3D/437' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=C2CCCCC2=NN1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113418.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113418/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113418 none O=C(CC1=C2CCCCC2=NN1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 5, 5, 5, 5, 1, 8, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 24, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 11, 11, 11, 29, 42, 42, 42, 42, 42, 11, 11, 1, 24, 24, 32, 32, 32, 32, 32, 32, 32, 32, 32, 6, 1, 1, 1, 1, 11, 29, 29, 42, 42, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 260 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113418 none O=C(CC1=C2CCCCC2=NN1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 5, 5, 5, 5, 1, 8, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 90, 121, 121, 121, 121, 121, 121, 121, 115, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 11, 90, 90, 121, 121, 121, 121, 121, 121, 121, 121, 121, 28, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 417 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113418 none O=C(CC1=C2CCCCC2=NN1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 5, 5, 5, 5, 1, 8, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 32, 32, 32, 121, 121, 121, 169, 201, 201, 201, 201, 201, 121, 121, 32, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 32, 32, 32, 32, 121, 169, 169, 201, 201, 32, 32] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 36, 38, 37, 39, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 666 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113418 none O=C(CC1=C2CCCCC2=NN1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 5, 5, 5, 5, 1, 8, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 169, 201, 201, 201, 201, 201, 201, 201, 192, 41, 41, 41, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 41, 169, 169, 201, 201, 201, 201, 201, 201, 201, 201, 201, 83, 41, 41, 41, 41, 9, 4, 4, 2, 2, 41, 41] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 696 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113418 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `2' /scratch/stefan/7770410/working/building/REAL300020113418/2 /scratch/stefan/7770410/working/building/REAL300020113418 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 2 (index: 438) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/438 `/scratch/stefan/7770410/working/3D/438' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=NNC2=C1CCCC2)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113418.mol2' -> `2.mol2' `temp.mol2' -> `REAL300020113418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113418/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113418 none O=C(CC1=NNC2=C1CCCC2)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 1, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 23, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 9, 9, 9, 32, 45, 48, 48, 48, 48, 9, 9, 1, 23, 23, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 9, 32, 32, 45, 45, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 270 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113418 none O=C(CC1=NNC2=C1CCCC2)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 1, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 91, 100, 100, 100, 100, 100, 100, 100, 100, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 91, 91, 100, 100, 100, 100, 100, 100, 100, 100, 100, 28, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 378 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113418 none O=C(CC1=NNC2=C1CCCC2)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 1, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 27, 27, 27, 100, 100, 100, 171, 201, 201, 201, 201, 201, 100, 100, 27, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 27, 27, 27, 27, 100, 171, 171, 201, 201, 27, 27] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 36, 38, 37, 39, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 722 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113418 none O=C(CC1=NNC2=C1CCCC2)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 1, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 189, 201, 201, 201, 201, 201, 201, 201, 201, 47, 47, 47, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 47, 189, 189, 201, 201, 201, 201, 201, 201, 201, 201, 201, 99, 47, 47, 47, 47, 10, 5, 5, 3, 3, 47, 47] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 720 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113418 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `3' /scratch/stefan/7770410/working/building/REAL300020113418/3 /scratch/stefan/7770410/working/building/REAL300020113418 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 3 (index: 439) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/439 `/scratch/stefan/7770410/working/3D/439' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=NNC2=C1CCCC2)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113418.mol2' -> `3.mol2' `temp.mol2' -> `REAL300020113418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113418/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113418 none O=C(CC1=NNC2=C1CCCC2)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 1, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 23, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 9, 9, 9, 32, 45, 48, 48, 48, 48, 9, 9, 1, 23, 23, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 9, 32, 32, 45, 45, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 270 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113418 none O=C(CC1=NNC2=C1CCCC2)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 1, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 92, 100, 100, 100, 100, 100, 100, 100, 100, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 92, 92, 100, 100, 100, 100, 100, 100, 100, 100, 100, 28, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 379 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113418 none O=C(CC1=NNC2=C1CCCC2)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 1, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 27, 27, 27, 100, 100, 100, 171, 201, 201, 201, 201, 201, 100, 100, 27, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 27, 27, 27, 27, 100, 171, 171, 201, 201, 27, 27] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 36, 38, 37, 39, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 723 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113418 none O=C(CC1=NNC2=C1CCCC2)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 1, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 190, 201, 201, 201, 201, 201, 201, 201, 201, 49, 49, 49, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 49, 190, 190, 201, 201, 201, 201, 201, 201, 201, 201, 201, 101, 49, 49, 49, 49, 13, 6, 6, 4, 4, 49, 49] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 718 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113418 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113418 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 2: /scratch/stefan/7770410/working/building/REAL300020113418/2.* 1: /scratch/stefan/7770410/working/building/REAL300020113418/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113418/0.* 3: /scratch/stefan/7770410/working/building/REAL300020113418/3.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113418 Building REAL300020113419 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113419' /scratch/stefan/7770410/working/building/REAL300020113419 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113419 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113419/0 /scratch/stefan/7770410/working/building/REAL300020113419 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/440 `/scratch/stefan/7770410/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC2=NNC=C21) `REAL300020113419.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113419 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC2=NNC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 1, 1, 13, 59, 124, 124, 124, 124, 124, 124, 124, 124, 59, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13, 124, 124, 124, 124, 124, 124, 124, 124, 124] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 395 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113419 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC2=NNC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [141, 141, 54, 54, 54, 10, 10, 10, 4, 2, 1, 1, 1, 1, 1, 1, 10, 10, 54, 141, 201, 201, 201, 201, 201, 201, 201, 201, 141, 54, 54, 54, 54, 10, 4, 4, 2, 2, 54, 54, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 593 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113419 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC2=NNC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 37, 54, 54, 54, 54, 54, 13, 13, 1, 6, 23, 23, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 13, 37, 37, 54, 54, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 274 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113419 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC2=NNC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 23, 23, 23, 124, 124, 124, 178, 201, 201, 201, 201, 201, 124, 124, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 23, 23, 23, 23, 124, 178, 178, 201, 201, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 603 number of broken/clashed sets: 8 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113419 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113419/1 /scratch/stefan/7770410/working/building/REAL300020113419 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 441) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/441 `/scratch/stefan/7770410/working/3D/441' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2=NNC=C21) `REAL300020113419.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113419 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2=NNC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 1, 1, 13, 59, 124, 124, 124, 124, 124, 124, 124, 124, 59, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13, 124, 124, 124, 124, 124, 124, 124, 124, 124] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 395 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113419 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2=NNC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [141, 141, 54, 54, 54, 10, 10, 10, 4, 2, 1, 1, 1, 1, 1, 1, 10, 10, 54, 141, 201, 201, 201, 201, 201, 201, 201, 201, 141, 54, 54, 54, 54, 10, 4, 4, 2, 2, 54, 54, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 593 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113419 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2=NNC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 37, 54, 54, 54, 54, 54, 13, 13, 1, 6, 23, 23, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 13, 37, 37, 54, 54, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 274 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113419 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2=NNC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 23, 23, 23, 124, 124, 124, 178, 201, 201, 201, 201, 201, 124, 124, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 23, 23, 23, 23, 124, 178, 178, 201, 201, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 603 number of broken/clashed sets: 8 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113419 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113419 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113419/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113419/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113419 Building REAL300020113420 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113420' /scratch/stefan/7770410/working/building/REAL300020113420 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113420 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113420/0 /scratch/stefan/7770410/working/building/REAL300020113420 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/442 `/scratch/stefan/7770410/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCC1) `REAL300020113420.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113420 none CCOCCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 52, 30, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 26, 37, 37, 37, 37, 37, 11, 11, 1, 21, 21, 21, 53, 53, 53, 53, 53, 30, 30, 21, 21, 6, 1, 1, 1, 1, 11, 26, 26, 37, 37, 1, 1, 21, 21, 21, 21, 21, 21] 201 rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 47, 48, 40, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50, 51, 52, 53, 54]) total number of confs: 303 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113420 none CCOCCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 140, 129, 129, 47, 47, 47, 11, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 11, 129, 129, 129, 157, 157, 157, 157, 157, 140, 140, 129, 129, 47, 11, 11, 11, 11, 1, 5, 5, 7, 7, 11, 11, 129, 129, 129, 129, 129, 129] 201 rigid atoms, others: [42, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 481 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113420 none CCOCCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 14, 5, 3, 1, 1, 1, 5, 5, 5, 21, 21, 21, 129, 129, 129, 159, 188, 188, 188, 188, 188, 129, 129, 21, 1, 1, 1, 15, 15, 15, 15, 15, 5, 5, 3, 3, 5, 21, 21, 21, 21, 129, 159, 159, 188, 188, 21, 21, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [4, 5, 6, 49, 50, 51, 52, 53, 54, 25, 26, 27] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 561 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113420 none CCOCCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 195, 195, 97, 97, 97, 40, 40, 40, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 40, 195, 195, 195, 201, 201, 201, 201, 201, 201, 201, 195, 195, 97, 40, 40, 40, 40, 7, 4, 4, 2, 2, 40, 40, 195, 195, 195, 195, 195, 195] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 596 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113420 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113420/1 /scratch/stefan/7770410/working/building/REAL300020113420 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 443) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/443 `/scratch/stefan/7770410/working/3D/443' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC1) `REAL300020113420.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113420/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113420 none CCOCCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 52, 30, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 26, 37, 37, 37, 37, 37, 11, 11, 1, 21, 21, 21, 53, 53, 53, 53, 53, 30, 30, 21, 21, 6, 1, 1, 1, 1, 11, 26, 26, 37, 37, 1, 1, 21, 21, 21, 21, 21, 21] 201 rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 47, 48, 40, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50, 51, 52, 53, 54]) total number of confs: 303 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113420 none CCOCCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 141, 130, 130, 47, 47, 47, 11, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 11, 130, 130, 130, 158, 158, 158, 158, 158, 141, 141, 130, 130, 47, 11, 11, 11, 11, 1, 5, 5, 7, 7, 11, 11, 130, 130, 130, 130, 130, 130] 201 rigid atoms, others: [42, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 483 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113420 none CCOCCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 14, 5, 3, 1, 1, 1, 5, 5, 5, 21, 21, 21, 130, 130, 130, 160, 188, 188, 188, 188, 188, 130, 130, 21, 1, 1, 1, 15, 15, 15, 15, 15, 5, 5, 3, 3, 5, 21, 21, 21, 21, 130, 160, 160, 188, 188, 21, 21, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [4, 5, 6, 49, 50, 51, 52, 53, 54, 25, 26, 27] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 556 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113420 none CCOCCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 195, 195, 98, 98, 98, 40, 40, 40, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 40, 195, 195, 195, 201, 201, 201, 201, 201, 201, 201, 195, 195, 98, 40, 40, 40, 40, 7, 4, 4, 2, 2, 40, 40, 195, 195, 195, 195, 195, 195] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 596 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113420 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113420 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113420/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113420/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113420 Building REAL300020113421 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113421' /scratch/stefan/7770410/working/building/REAL300020113421 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113421 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113421/0 /scratch/stefan/7770410/working/building/REAL300020113421 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/444 `/scratch/stefan/7770410/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1CC1CCC1) `REAL300020113421.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113421 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1CC1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 5, 5, 5, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 5, 19, 48, 48, 48, 48, 48, 94, 120, 120, 120, 19, 5, 5, 5, 5, 1, 6, 6, 8, 8, 5, 5, 48, 48, 94, 94, 120, 120, 120, 120, 120, 120, 120] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 456 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113421 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1CC1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 12, 26, 26, 69, 69, 69, 120, 120, 120, 169, 201, 201, 201, 201, 201, 120, 120, 69, 12, 12, 12, 12, 6, 1, 1, 1, 1, 1, 26, 69, 69, 69, 69, 120, 169, 169, 201, 201, 69, 69, 12, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 699 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113421 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1CC1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 26, 26, 26, 9, 9, 9, 5, 2, 1, 1, 1, 1, 1, 1, 9, 9, 26, 51, 89, 89, 89, 89, 89, 168, 201, 201, 201, 51, 26, 26, 26, 26, 9, 5, 5, 2, 2, 26, 26, 89, 89, 168, 168, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 761 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113421 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1CC1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 16, 24, 24, 24, 24, 24, 5, 5, 1, 6, 19, 19, 19, 19, 19, 47, 69, 69, 69, 6, 1, 1, 1, 1, 5, 16, 16, 24, 24, 1, 1, 19, 19, 47, 47, 69, 69, 69, 69, 69, 69, 69] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 345 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113421 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1CC1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 19, 19, 19, 48, 48, 48, 73, 89, 89, 89, 89, 89, 48, 48, 19, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 6, 19, 19, 19, 19, 48, 73, 73, 89, 89, 19, 19, 1, 1, 6, 6, 12, 12, 12, 12, 12, 12, 12] 201 rigid atoms, others: [1, 41, 42, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 343 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113421 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113421/1 /scratch/stefan/7770410/working/building/REAL300020113421 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 445) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/445 `/scratch/stefan/7770410/working/3D/445' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1CC1CCC1) `REAL300020113421.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113421 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1CC1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 5, 5, 5, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 5, 19, 48, 48, 48, 48, 48, 94, 120, 120, 120, 19, 5, 5, 5, 5, 1, 6, 6, 8, 8, 5, 5, 48, 48, 94, 94, 120, 120, 120, 120, 120, 120, 120] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 456 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113421 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1CC1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 12, 26, 26, 69, 69, 69, 120, 120, 120, 169, 201, 201, 201, 201, 201, 120, 120, 69, 12, 12, 12, 12, 6, 1, 1, 1, 1, 1, 26, 69, 69, 69, 69, 120, 169, 169, 201, 201, 69, 69, 12, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 699 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113421 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1CC1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 26, 26, 26, 9, 9, 9, 5, 2, 1, 1, 1, 1, 1, 1, 9, 9, 26, 51, 89, 89, 89, 89, 89, 168, 201, 201, 201, 51, 26, 26, 26, 26, 9, 5, 5, 2, 2, 26, 26, 89, 89, 168, 168, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 761 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113421 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1CC1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 17, 25, 25, 25, 25, 25, 5, 5, 1, 6, 19, 19, 19, 19, 19, 47, 69, 69, 69, 6, 1, 1, 1, 1, 5, 17, 17, 25, 25, 1, 1, 19, 19, 47, 47, 69, 69, 69, 69, 69, 69, 69] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 348 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113421 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1CC1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 19, 19, 19, 48, 48, 48, 74, 90, 90, 90, 90, 90, 48, 48, 19, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 6, 19, 19, 19, 19, 48, 74, 74, 90, 90, 19, 19, 1, 1, 6, 6, 12, 12, 12, 12, 12, 12, 12] 201 rigid atoms, others: [1, 41, 42, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 346 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113421 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113421 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113421/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113421/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113421 Building REAL300020113422 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113422' /scratch/stefan/7770410/working/building/REAL300020113422 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113422 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113422/0 /scratch/stefan/7770410/working/building/REAL300020113422 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/446 `/scratch/stefan/7770410/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC1) `REAL300020113422.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113422 none CCOC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 27, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 3, 27, 36, 36, 34, 34, 34, 34, 34, 27, 8, 3, 3, 3, 3, 1, 5, 5, 5, 5, 3, 3, 36, 36, 36, 36, 36] 42 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 155 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113422 none CCOC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 33, 14, 14, 14, 7, 7, 7, 7, 7, 7, 5, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 33, 41, 41, 37, 37, 37, 37, 37, 33, 14, 7, 7, 7, 7, 7, 5, 5, 2, 2, 7, 7, 41, 41, 41, 41, 41] 42 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 167 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113422 none CCOC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 26, 6, 6, 6, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 3, 3, 1, 26, 36, 36, 33, 33, 33, 33, 33, 26, 6, 1, 1, 1, 1, 3, 5, 5, 5, 5, 1, 1, 36, 36, 36, 36, 36] 42 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113422 none CCOC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 8, 1, 8, 25, 25, 25, 36, 36, 36, 36, 36, 36, 41, 41, 41, 41, 41, 41, 36, 36, 36, 1, 1, 1, 16, 16, 16, 16, 16, 8, 25, 36, 36, 36, 36, 36, 41, 41, 41, 41, 36, 36, 1, 1, 1, 1, 1] 42 rigid atoms, others: [3, 44, 45, 46, 47, 48, 23, 24, 25] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 149 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113422 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113422/1 /scratch/stefan/7770410/working/building/REAL300020113422 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 447) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/447 `/scratch/stefan/7770410/working/3D/447' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC1) `REAL300020113422.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113422 none CCOC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 27, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 3, 27, 36, 36, 34, 34, 34, 34, 34, 27, 8, 3, 3, 3, 3, 1, 5, 5, 5, 5, 3, 3, 36, 36, 36, 36, 36] 42 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 155 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113422 none CCOC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 33, 14, 14, 14, 7, 7, 7, 7, 7, 7, 5, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 33, 41, 41, 37, 37, 37, 37, 37, 33, 14, 7, 7, 7, 7, 7, 5, 5, 2, 2, 7, 7, 41, 41, 41, 41, 41] 42 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 167 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113422 none CCOC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 26, 6, 6, 6, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 3, 3, 1, 26, 36, 36, 33, 33, 33, 33, 33, 26, 6, 1, 1, 1, 1, 3, 5, 5, 5, 5, 1, 1, 36, 36, 36, 36, 36] 42 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113422 none CCOC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 8, 1, 8, 25, 25, 25, 36, 36, 36, 36, 36, 36, 41, 41, 41, 41, 41, 41, 36, 36, 36, 1, 1, 1, 16, 16, 16, 16, 16, 8, 25, 36, 36, 36, 36, 36, 41, 41, 41, 41, 36, 36, 1, 1, 1, 1, 1] 42 rigid atoms, others: [3, 44, 45, 46, 47, 48, 23, 24, 25] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 149 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113422 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113422 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113422/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113422/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113422 Building REAL300020113423 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113423' /scratch/stefan/7770410/working/building/REAL300020113423 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113423 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113423/0 /scratch/stefan/7770410/working/building/REAL300020113423 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/448 `/scratch/stefan/7770410/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)OC(CC2CC2)=N1) `REAL300020113423.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113423 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)OC(CC2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 15, 24, 24, 24, 24, 24, 9, 9, 1, 14, 14, 14, 35, 52, 52, 14, 14, 14, 14, 6, 1, 1, 1, 1, 9, 15, 15, 24, 24, 1, 1, 35, 35, 52, 52, 52, 52, 52] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 42, 43, 21] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 295 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113423 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)OC(CC2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 8, 18, 18, 18, 52, 52, 52, 150, 150, 150, 177, 201, 201, 201, 201, 201, 150, 150, 52, 8, 3, 1, 1, 1, 1, 8, 8, 8, 8, 18, 52, 52, 52, 52, 150, 177, 177, 201, 201, 52, 52, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [46, 47, 48, 49, 50, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 579 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113423 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)OC(CC2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 33, 33, 33, 9, 9, 9, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 1, 1, 9, 62, 62, 62, 112, 150, 150, 62, 62, 62, 62, 33, 9, 9, 9, 9, 1, 3, 3, 5, 5, 9, 9, 112, 112, 150, 150, 150, 150, 150] 201 rigid atoms, others: [37, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 593 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113423 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)OC(CC2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 62, 62, 62, 79, 99, 99, 99, 99, 99, 62, 62, 14, 1, 1, 1, 4, 8, 8, 1, 2, 2, 2, 4, 14, 14, 14, 14, 62, 79, 79, 99, 99, 14, 14, 4, 4, 8, 8, 8, 8, 8] 201 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24, 28] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 347 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113423 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)OC(CC2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 75, 75, 75, 28, 28, 28, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 28, 107, 107, 107, 173, 201, 201, 107, 107, 107, 107, 75, 28, 28, 28, 28, 7, 4, 4, 2, 2, 28, 28, 173, 173, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 771 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113423 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113423/1 /scratch/stefan/7770410/working/building/REAL300020113423 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 449) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/449 `/scratch/stefan/7770410/working/3D/449' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)OC(CC2CC2)=N1) `REAL300020113423.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113423/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113423 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)OC(CC2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 15, 24, 24, 24, 24, 24, 9, 9, 1, 14, 14, 14, 35, 52, 52, 14, 14, 14, 14, 6, 1, 1, 1, 1, 9, 15, 15, 24, 24, 1, 1, 35, 35, 52, 52, 52, 52, 52] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 42, 43, 21] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 295 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113423 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)OC(CC2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 8, 18, 18, 18, 52, 52, 52, 149, 149, 149, 176, 201, 201, 201, 201, 201, 149, 149, 52, 8, 3, 1, 1, 1, 1, 8, 8, 8, 8, 18, 52, 52, 52, 52, 149, 176, 176, 201, 201, 52, 52, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [46, 47, 48, 49, 50, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 584 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113423 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)OC(CC2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 33, 33, 33, 9, 9, 9, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 1, 1, 9, 62, 62, 62, 112, 149, 149, 62, 62, 62, 62, 33, 9, 9, 9, 9, 1, 3, 3, 5, 5, 9, 9, 112, 112, 149, 149, 149, 149, 149] 201 rigid atoms, others: [37, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 589 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113423 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)OC(CC2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 62, 62, 62, 78, 98, 98, 98, 98, 98, 62, 62, 14, 1, 1, 1, 4, 8, 8, 1, 2, 2, 2, 4, 14, 14, 14, 14, 62, 78, 78, 98, 98, 14, 14, 4, 4, 8, 8, 8, 8, 8] 201 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24, 28] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113423 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)OC(CC2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 75, 75, 75, 28, 28, 28, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 28, 107, 107, 107, 173, 201, 201, 107, 107, 107, 107, 75, 28, 28, 28, 28, 7, 4, 4, 2, 2, 28, 28, 173, 173, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 771 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113423 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113423 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113423/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113423/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113423 Building REAL300020113424 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113424' /scratch/stefan/7770410/working/building/REAL300020113424 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113424 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113424/0 /scratch/stefan/7770410/working/building/REAL300020113424 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/450 `/scratch/stefan/7770410/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCOCC(F)F)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113424.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113424 none O=C(CCOCC(F)F)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 15, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 64, 69, 76, 126, 139, 139, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 64, 64, 69, 69, 126, 126, 139, 14, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 613 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113424 none O=C(CCOCC(F)F)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 15, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 121, 122, 131, 201, 201, 201, 32, 32, 32, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 32, 121, 121, 122, 122, 201, 201, 201, 42, 32, 32, 32, 32, 7, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 801 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113424 none O=C(CCOCC(F)F)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 15, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 19, 22, 29, 47, 56, 56, 1, 1, 1, 1, 1, 8, 8, 8, 22, 34, 34, 34, 34, 34, 8, 8, 1, 19, 19, 22, 22, 47, 47, 56, 3, 1, 1, 1, 1, 8, 22, 22, 34, 34, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 368 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113424 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113424/1 /scratch/stefan/7770410/working/building/REAL300020113424 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 451) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/451 `/scratch/stefan/7770410/working/3D/451' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCOCC(F)F)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113424.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113424 none O=C(CCOCC(F)F)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 15, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 63, 68, 75, 126, 139, 139, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 63, 63, 68, 68, 126, 126, 139, 13, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7] 201 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 617 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113424 none O=C(CCOCC(F)F)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 15, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 121, 121, 129, 201, 201, 201, 32, 32, 32, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 32, 121, 121, 121, 121, 201, 201, 201, 42, 32, 32, 32, 32, 7, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 801 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113424 none O=C(CCOCC(F)F)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 15, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 19, 22, 29, 47, 56, 56, 1, 1, 1, 1, 1, 7, 7, 7, 21, 33, 33, 33, 33, 33, 7, 7, 1, 19, 19, 22, 22, 47, 47, 56, 3, 1, 1, 1, 1, 7, 21, 21, 33, 33, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 367 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113424 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113424 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113424/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113424/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113424 Building REAL300020113425 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113425' /scratch/stefan/7770410/working/building/REAL300020113425 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113425 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113425/0 /scratch/stefan/7770410/working/building/REAL300020113425 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/452 `/scratch/stefan/7770410/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1N=CN=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113425.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113425 none O=C(CN1N=CN=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 8, 1, 8, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 20, 37, 37, 37, 37, 1, 1, 1, 1, 1, 9, 9, 9, 24, 36, 37, 37, 37, 37, 9, 9, 1, 20, 20, 37, 6, 1, 1, 1, 1, 9, 24, 24, 36, 36, 1, 1] 201 rigid atoms, others: [32, 38, 39, 8, 9, 10, 11, 12, 24, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 33, 34, 35, 36, 37]) total number of confs: 238 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113425 none O=C(CN1N=CN=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 8, 1, 8, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 61, 109, 109, 109, 109, 9, 9, 9, 1, 1, 1, 1, 1, 5, 7, 8, 8, 8, 8, 1, 1, 9, 61, 61, 109, 21, 9, 9, 9, 9, 1, 5, 5, 7, 7, 9, 9] 201 rigid atoms, others: [33, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39]) total number of confs: 338 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113425 none O=C(CN1N=CN=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 8, 1, 8, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 7, 1, 1, 1, 1, 1, 1, 24, 24, 37, 37, 37, 109, 109, 109, 169, 201, 201, 201, 201, 201, 109, 109, 37, 7, 7, 1, 24, 37, 37, 37, 37, 109, 169, 169, 201, 201, 37, 37] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 27] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 700 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113425 none O=C(CN1N=CN=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 8, 1, 8, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 116, 201, 201, 201, 201, 37, 37, 37, 8, 8, 8, 5, 3, 1, 1, 1, 1, 1, 1, 8, 8, 37, 116, 116, 201, 61, 37, 37, 37, 37, 8, 5, 5, 3, 3, 37, 37] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 617 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113425 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113425/1 /scratch/stefan/7770410/working/building/REAL300020113425 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 453) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/453 `/scratch/stefan/7770410/working/3D/453' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1N=CN=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113425.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113425/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113425 none O=C(CN1N=CN=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 8, 1, 8, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 19, 36, 36, 36, 36, 1, 1, 1, 1, 1, 9, 9, 9, 24, 36, 37, 37, 37, 37, 9, 9, 1, 19, 19, 36, 6, 1, 1, 1, 1, 9, 24, 24, 36, 36, 1, 1] 201 rigid atoms, others: [32, 38, 39, 8, 9, 10, 11, 12, 24, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 33, 34, 35, 36, 37]) total number of confs: 235 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113425 none O=C(CN1N=CN=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 8, 1, 8, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 61, 108, 108, 108, 108, 9, 9, 9, 1, 1, 1, 1, 1, 5, 7, 8, 8, 8, 8, 1, 1, 9, 61, 61, 108, 21, 9, 9, 9, 9, 1, 5, 5, 7, 7, 9, 9] 201 rigid atoms, others: [33, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39]) total number of confs: 336 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113425 none O=C(CN1N=CN=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 8, 1, 8, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 7, 1, 1, 1, 1, 1, 1, 22, 22, 36, 36, 36, 108, 108, 108, 169, 201, 201, 201, 201, 201, 108, 108, 36, 7, 7, 1, 22, 36, 36, 36, 36, 108, 169, 169, 201, 201, 36, 36] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 27] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 705 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113425 none O=C(CN1N=CN=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 8, 1, 8, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 117, 201, 201, 201, 201, 37, 37, 37, 8, 8, 8, 5, 3, 1, 1, 1, 1, 1, 1, 8, 8, 37, 117, 117, 201, 62, 37, 37, 37, 37, 8, 5, 5, 3, 3, 37, 37] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 620 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113425 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113425 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113425/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113425/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113425 Building REAL300020113426 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113426' /scratch/stefan/7770410/working/building/REAL300020113426 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113426 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113426/0 /scratch/stefan/7770410/working/building/REAL300020113426 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/454 `/scratch/stefan/7770410/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(Cl)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113426.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113426 none CN1N=CC(Cl)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 36, 53, 64, 64, 64, 64, 11, 11, 1, 15, 15, 15, 15, 6, 1, 1, 1, 1, 11, 36, 36, 53, 53, 1, 1] 201 rigid atoms, others: [32, 33, 34, 40, 9, 10, 11, 12, 13, 41, 25, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) total number of confs: 267 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113426 none CN1N=CC(Cl)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 81, 81, 81, 43, 43, 43, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 81, 81, 81, 81, 43, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11] 201 rigid atoms, others: [35, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 216 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113426 none CN1N=CC(Cl)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 81, 81, 81, 150, 201, 201, 201, 201, 201, 81, 81, 15, 2, 2, 2, 1, 5, 15, 15, 15, 15, 81, 150, 150, 201, 201, 15, 15] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 790 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113426 none CN1N=CC(Cl)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 123, 123, 123, 64, 64, 64, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 64, 201, 201, 201, 201, 123, 64, 64, 64, 64, 11, 6, 6, 4, 4, 64, 64] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 504 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113426 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113426/1 /scratch/stefan/7770410/working/building/REAL300020113426 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 455) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/455 `/scratch/stefan/7770410/working/3D/455' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(Cl)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113426.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113426 none CN1N=CC(Cl)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 37, 54, 65, 65, 65, 65, 11, 11, 1, 15, 15, 15, 15, 6, 1, 1, 1, 1, 11, 37, 37, 54, 54, 1, 1] 201 rigid atoms, others: [32, 33, 34, 40, 9, 10, 11, 12, 13, 41, 25, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) total number of confs: 270 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113426 none CN1N=CC(Cl)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 78, 78, 78, 42, 42, 42, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 78, 78, 78, 78, 42, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11] 201 rigid atoms, others: [35, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 213 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113426 none CN1N=CC(Cl)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 78, 78, 78, 149, 201, 201, 201, 201, 201, 78, 78, 15, 2, 2, 2, 1, 5, 15, 15, 15, 15, 78, 149, 149, 201, 201, 15, 15] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 802 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113426 none CN1N=CC(Cl)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 124, 124, 124, 66, 66, 66, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 66, 201, 201, 201, 201, 124, 66, 66, 66, 66, 12, 6, 6, 4, 4, 66, 66] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 503 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113426 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113426 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113426/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113426/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113426 Building REAL300020113427 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113427' /scratch/stefan/7770410/working/building/REAL300020113427 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113427 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113427/0 /scratch/stefan/7770410/working/building/REAL300020113427 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/456 `/scratch/stefan/7770410/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NC=N1) `REAL300020113427.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113427 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 53, 75, 91, 91, 91, 91, 13, 13, 1, 11, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 13, 53, 53, 75, 75, 1, 1, 11] 201 rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43]) total number of confs: 355 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113427 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 82, 58, 58, 58, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 13, 82, 82, 82, 82, 82, 82, 82, 58, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13, 82] 201 rigid atoms, others: [36, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 233 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113427 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 82, 82, 82, 168, 201, 201, 201, 201, 201, 82, 82, 11, 1, 1, 1, 2, 2, 2, 1, 3, 11, 11, 11, 11, 82, 168, 168, 201, 201, 11, 11, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 24, 25, 26, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 745 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113427 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 200, 200, 200, 91, 91, 91, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 91, 201, 201, 201, 201, 201, 201, 201, 200, 91, 91, 91, 91, 14, 6, 6, 4, 4, 91, 91, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 557 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113427 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113427/1 /scratch/stefan/7770410/working/building/REAL300020113427 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 457) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/457 `/scratch/stefan/7770410/working/3D/457' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NC=N1) `REAL300020113427.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113427/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113427 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 52, 74, 89, 89, 89, 89, 13, 13, 1, 11, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 13, 52, 52, 74, 74, 1, 1, 11] 201 rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43]) total number of confs: 350 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113427 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 82, 57, 57, 57, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 13, 82, 82, 82, 82, 82, 82, 82, 57, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13, 82] 201 rigid atoms, others: [36, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 233 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113427 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 82, 82, 82, 166, 201, 201, 201, 201, 201, 82, 82, 11, 1, 1, 1, 2, 2, 2, 1, 3, 11, 11, 11, 11, 82, 166, 166, 201, 201, 11, 11, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 24, 25, 26, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 748 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113427 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 200, 200, 200, 89, 89, 89, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 89, 201, 201, 201, 201, 201, 201, 201, 200, 89, 89, 89, 89, 14, 6, 6, 4, 4, 89, 89, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 557 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113427 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113427 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113427/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113427/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113427 Building REAL300020113428 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113428' /scratch/stefan/7770410/working/building/REAL300020113428 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113428 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113428/0 /scratch/stefan/7770410/working/building/REAL300020113428 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/458 `/scratch/stefan/7770410/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1C[NH+]2CCC1CC2) `REAL300020113428.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113428 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1C[NH+]2CCC1CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 13, 13, 13, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 13, 42, 52, 52, 52, 52, 52, 52, 52, 52, 42, 13, 13, 13, 13, 1, 5, 5, 5, 5, 13, 13, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52] 63 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 160 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113428 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1C[NH+]2CCC1CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 27, 27, 27, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 27, 60, 63, 63, 63, 63, 63, 63, 63, 63, 60, 27, 27, 27, 27, 5, 3, 3, 1, 1, 27, 27, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63] 63 rigid atoms, others: [36, 37, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 176 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113428 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1C[NH+]2CCC1CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 27, 27, 27, 27, 27, 27, 13, 13, 1, 6, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 13, 27, 27, 27, 27, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 63 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113428 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1C[NH+]2CCC1CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 15, 15, 15, 52, 52, 52, 63, 63, 63, 63, 63, 63, 52, 52, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 15, 52, 63, 63, 63, 63, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 63 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 27, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 149 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113428 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113428/1 /scratch/stefan/7770410/working/building/REAL300020113428 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 459) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/459 `/scratch/stefan/7770410/working/3D/459' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1C[NH+]2CCC1CC2) `REAL300020113428.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113428/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113428 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1C[NH+]2CCC1CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 13, 13, 13, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 13, 42, 52, 52, 52, 52, 52, 52, 52, 52, 42, 13, 13, 13, 13, 1, 5, 5, 5, 5, 13, 13, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52] 63 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 160 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113428 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1C[NH+]2CCC1CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 27, 27, 27, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 27, 60, 63, 63, 63, 63, 63, 63, 63, 63, 60, 27, 27, 27, 27, 5, 3, 3, 1, 1, 27, 27, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63] 63 rigid atoms, others: [36, 37, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 176 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113428 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1C[NH+]2CCC1CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 27, 27, 27, 27, 27, 27, 13, 13, 1, 6, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 13, 27, 27, 27, 27, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 63 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113428 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1C[NH+]2CCC1CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 15, 15, 15, 52, 52, 52, 63, 63, 63, 63, 63, 63, 52, 52, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 15, 52, 63, 63, 63, 63, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 63 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 27, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 149 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113428 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113428 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113428/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113428/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113428 Building REAL300020113429 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113429' /scratch/stefan/7770410/working/building/REAL300020113429 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113429 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113429/0 /scratch/stefan/7770410/working/building/REAL300020113429 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/460 `/scratch/stefan/7770410/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@@H](C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113429.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113429 none CCCC[C@@H](C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 101, 70, 18, 70, 70, 18, 18, 5, 5, 5, 1, 1, 1, 1, 1, 8, 10, 14, 14, 14, 14, 1, 1, 5, 103, 103, 103, 103, 103, 103, 103, 102, 102, 70, 70, 70, 18, 5, 5, 5, 5, 1, 8, 8, 10, 10, 5, 5] 201 rigid atoms, others: [43, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 474 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113429 none CCCC[C@@H](C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 165, 79, 165, 165, 79, 79, 41, 41, 41, 17, 17, 17, 7, 4, 1, 1, 1, 1, 1, 1, 17, 17, 41, 201, 201, 201, 201, 201, 201, 201, 201, 201, 165, 165, 165, 79, 41, 41, 41, 41, 17, 7, 7, 4, 4, 41, 41] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 804 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113429 none CCCC[C@@H](C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 56, 54, 30, 6, 30, 30, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 21, 29, 35, 35, 35, 35, 5, 5, 1, 61, 61, 61, 61, 61, 56, 56, 55, 55, 30, 30, 30, 6, 1, 1, 1, 1, 5, 21, 21, 29, 29, 1, 1] 201 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 48, 49, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 401 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113429 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113429/1 /scratch/stefan/7770410/working/building/REAL300020113429 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 461) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/461 `/scratch/stefan/7770410/working/3D/461' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@@H](C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113429.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113429 none CCCC[C@@H](C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 101, 70, 18, 70, 70, 18, 18, 5, 5, 5, 1, 1, 1, 1, 1, 8, 10, 14, 14, 14, 14, 1, 1, 5, 103, 103, 103, 103, 103, 103, 103, 102, 102, 70, 70, 70, 18, 5, 5, 5, 5, 1, 8, 8, 10, 10, 5, 5] 201 rigid atoms, others: [43, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 474 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113429 none CCCC[C@@H](C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 165, 78, 165, 165, 78, 78, 40, 40, 40, 16, 16, 16, 7, 4, 1, 1, 1, 1, 1, 1, 16, 16, 40, 201, 201, 201, 201, 201, 201, 201, 201, 201, 165, 165, 165, 78, 40, 40, 40, 40, 16, 7, 7, 4, 4, 40, 40] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 806 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113429 none CCCC[C@@H](C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 56, 54, 30, 6, 30, 30, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 22, 30, 35, 35, 35, 35, 5, 5, 1, 61, 61, 61, 61, 61, 56, 56, 55, 55, 30, 30, 30, 6, 1, 1, 1, 1, 5, 22, 22, 30, 30, 1, 1] 201 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 48, 49, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 402 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113429 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113429 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113429/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113429/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113429 Building REAL300020113430 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113430' /scratch/stefan/7770410/working/building/REAL300020113430 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113430 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113430/0 /scratch/stefan/7770410/working/building/REAL300020113430 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/462 `/scratch/stefan/7770410/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020113430.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113430 none CCC1=CC=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 8, 8, 8, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 35, 53, 62, 62, 62, 62, 11, 11, 1, 8, 15, 15, 15, 15, 15, 8, 8, 6, 1, 1, 1, 1, 11, 35, 35, 53, 53, 1, 1, 8] 201 rigid atoms, others: [45, 35, 36, 37, 38, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46]) total number of confs: 298 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113430 none CCC1=CC=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 49, 49, 49, 49, 49, 46, 46, 46, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 49, 96, 96, 96, 96, 96, 49, 49, 46, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 49] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 435 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113430 none CCC1=CC=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 49, 49, 49, 90, 105, 105, 105, 105, 105, 49, 49, 8, 1, 2, 2, 2, 2, 2, 1, 1, 4, 8, 8, 8, 8, 49, 90, 90, 105, 105, 8, 8, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 46, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 375 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113430 none CCC1=CC=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 105, 105, 105, 105, 105, 105, 105, 105, 62, 62, 62, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 62, 105, 201, 201, 201, 201, 201, 105, 105, 105, 62, 62, 62, 62, 10, 6, 6, 4, 4, 62, 62, 105] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 881 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113430 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113430/1 /scratch/stefan/7770410/working/building/REAL300020113430 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 463) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/463 `/scratch/stefan/7770410/working/3D/463' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020113430.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113430 none CCC1=CC=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 8, 8, 8, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 35, 53, 62, 62, 62, 62, 11, 11, 1, 8, 15, 15, 15, 15, 15, 8, 8, 6, 1, 1, 1, 1, 11, 35, 35, 53, 53, 1, 1, 8] 201 rigid atoms, others: [45, 35, 36, 37, 38, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46]) total number of confs: 298 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113430 none CCC1=CC=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 49, 49, 49, 49, 49, 46, 46, 46, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 49, 96, 96, 96, 96, 96, 49, 49, 46, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 49] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 435 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113430 none CCC1=CC=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 49, 49, 49, 90, 104, 104, 104, 104, 104, 49, 49, 8, 1, 2, 2, 2, 2, 2, 1, 1, 4, 8, 8, 8, 8, 49, 90, 90, 104, 104, 8, 8, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 46, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 369 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113430 none CCC1=CC=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 105, 105, 105, 105, 105, 105, 105, 105, 63, 63, 63, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 63, 105, 201, 201, 201, 201, 201, 105, 105, 105, 63, 63, 63, 63, 11, 6, 6, 4, 4, 63, 63, 105] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 881 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113430 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113430 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113430/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113430/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113430 Building REAL300020113431 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113431' /scratch/stefan/7770410/working/building/REAL300020113431 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113431 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113431/0 /scratch/stefan/7770410/working/building/REAL300020113431 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/464 `/scratch/stefan/7770410/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CC2=CC=CC=C2O1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113431.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113431 none O=C(CC1CC2=CC=CC=C2O1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 28, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 9, 9, 9, 29, 42, 43, 43, 43, 43, 9, 9, 1, 28, 28, 37, 37, 37, 37, 37, 37, 37, 6, 1, 1, 1, 1, 9, 29, 29, 42, 42, 1, 1] 201 rigid atoms, others: [48, 39, 40, 41, 42, 12, 13, 14, 15, 16, 49, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 296 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113431 none O=C(CC1CC2=CC=CC=C2O1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 96, 114, 114, 114, 114, 114, 114, 114, 114, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 9, 96, 96, 114, 114, 114, 114, 114, 114, 114, 26, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [43, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 424 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113431 none O=C(CC1CC2=CC=CC=C2O1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 37, 37, 37, 114, 114, 114, 163, 201, 201, 201, 201, 201, 114, 114, 37, 7, 7, 1, 1, 1, 1, 1, 1, 1, 18, 37, 37, 37, 37, 114, 163, 163, 201, 201, 37, 37] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 36, 37, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 712 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113431 none O=C(CC1CC2=CC=CC=C2O1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 190, 201, 201, 201, 201, 201, 201, 201, 201, 43, 43, 43, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 43, 190, 190, 201, 201, 201, 201, 201, 201, 201, 76, 43, 43, 43, 43, 9, 5, 5, 3, 3, 43, 43] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 731 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113431 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113431/1 /scratch/stefan/7770410/working/building/REAL300020113431 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 465) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/465 `/scratch/stefan/7770410/working/3D/465' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CC2=CC=CC=C2O1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113431.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113431 none O=C(CC1CC2=CC=CC=C2O1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 28, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 8, 8, 8, 28, 41, 42, 42, 42, 42, 8, 8, 1, 28, 28, 37, 37, 37, 37, 37, 37, 37, 6, 1, 1, 1, 1, 8, 28, 28, 41, 41, 1, 1] 201 rigid atoms, others: [48, 39, 40, 41, 42, 12, 13, 14, 15, 16, 49, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 295 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113431 none O=C(CC1CC2=CC=CC=C2O1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 95, 113, 113, 113, 113, 113, 113, 113, 113, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 95, 95, 113, 113, 113, 113, 113, 113, 113, 25, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [43, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 422 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113431 none O=C(CC1CC2=CC=CC=C2O1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 37, 37, 37, 113, 113, 113, 162, 201, 201, 201, 201, 201, 113, 113, 37, 7, 7, 1, 1, 1, 1, 1, 1, 1, 18, 37, 37, 37, 37, 113, 162, 162, 201, 201, 37, 37] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 36, 37, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 717 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113431 none O=C(CC1CC2=CC=CC=C2O1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 191, 201, 201, 201, 201, 201, 201, 201, 201, 42, 42, 42, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 42, 191, 191, 201, 201, 201, 201, 201, 201, 201, 75, 42, 42, 42, 42, 9, 5, 5, 3, 3, 42, 42] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 731 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113431 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113431 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113431/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113431/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113431 Building REAL300020113432 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113432' /scratch/stefan/7770410/working/building/REAL300020113432 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113432 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113432/0 /scratch/stefan/7770410/working/building/REAL300020113432 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/466 `/scratch/stefan/7770410/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=NNN=C21) `REAL300020113432.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113432 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=NNN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 8, 12, 16, 16, 16, 16, 1, 1, 6, 22, 78, 78, 78, 78, 78, 78, 78, 78, 22, 6, 6, 6, 6, 1, 8, 8, 12, 12, 6, 6, 78, 78, 78, 78] 138 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 183 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113432 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=NNN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 46, 46, 46, 18, 18, 18, 7, 4, 1, 1, 1, 1, 1, 1, 18, 18, 46, 83, 138, 138, 138, 138, 138, 138, 138, 138, 83, 46, 46, 46, 46, 18, 7, 7, 4, 4, 46, 46, 138, 138, 138, 138] 138 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 335 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113432 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=NNN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 27, 36, 45, 45, 45, 45, 6, 6, 1, 6, 43, 43, 43, 43, 43, 43, 43, 43, 6, 1, 1, 1, 1, 6, 27, 27, 36, 36, 1, 1, 43, 43, 43, 43] 138 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 211 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113432 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=NNN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 43, 43, 43, 78, 78, 78, 127, 138, 138, 138, 138, 138, 78, 78, 43, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 43, 43, 43, 43, 78, 127, 127, 138, 138, 43, 43, 1, 1, 1, 1] 138 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 473 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113432 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113432/1 /scratch/stefan/7770410/working/building/REAL300020113432 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 467) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/467 `/scratch/stefan/7770410/working/3D/467' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=NNN=C21) `REAL300020113432.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113432/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113432 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=NNN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 8, 12, 16, 16, 16, 16, 1, 1, 6, 22, 77, 77, 77, 77, 77, 77, 77, 77, 22, 6, 6, 6, 6, 1, 8, 8, 12, 12, 6, 6, 77, 77, 77, 77] 137 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 182 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113432 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=NNN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 46, 46, 46, 18, 18, 18, 7, 4, 1, 1, 1, 1, 1, 1, 18, 18, 46, 83, 138, 138, 138, 138, 138, 138, 138, 138, 83, 46, 46, 46, 46, 18, 7, 7, 4, 4, 46, 46, 138, 138, 138, 138] 138 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 335 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113432 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=NNN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 26, 35, 43, 43, 43, 43, 6, 6, 1, 6, 41, 41, 41, 41, 41, 41, 41, 41, 6, 1, 1, 1, 1, 6, 26, 26, 35, 35, 1, 1, 41, 41, 41, 41] 137 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 204 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113432 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=NNN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 41, 41, 41, 77, 77, 77, 126, 137, 137, 137, 137, 137, 77, 77, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 41, 41, 41, 41, 77, 126, 126, 137, 137, 41, 41, 1, 1, 1, 1] 137 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 471 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113432 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113432 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113432/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113432/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113432 Building REAL300020113433 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113433' /scratch/stefan/7770410/working/building/REAL300020113433 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113433 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113433/0 /scratch/stefan/7770410/working/building/REAL300020113433 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/468 `/scratch/stefan/7770410/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1) `REAL300020113433.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113433 none CC1=C(C)CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 27, 40, 43, 43, 43, 43, 10, 10, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 10, 27, 27, 40, 40, 1, 1, 22, 22, 22, 22] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 46, 47, 40, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 218 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113433 none CC1=C(C)CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 95, 95, 28, 28, 28, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 10, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 28, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 95, 95, 95, 95] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 279 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113433 none CC1=C(C)CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 8, 22, 22, 22, 95, 95, 95, 157, 201, 201, 201, 201, 201, 95, 95, 22, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 8, 22, 22, 22, 22, 95, 157, 157, 201, 201, 22, 22, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 34, 48, 49, 50, 35, 25, 26, 51] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 751 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113433 none CC1=C(C)CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 88, 88, 88, 45, 45, 45, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 45, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 88, 45, 45, 45, 45, 12, 6, 6, 4, 4, 45, 45, 201, 201, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 584 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113433 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113433/1 /scratch/stefan/7770410/working/building/REAL300020113433 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 469) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/469 `/scratch/stefan/7770410/working/3D/469' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1) `REAL300020113433.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113433/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113433 none CC1=C(C)CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 27, 40, 44, 44, 44, 44, 10, 10, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 10, 27, 27, 40, 40, 1, 1, 22, 22, 22, 22] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 46, 47, 40, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 220 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113433 none CC1=C(C)CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 96, 96, 28, 28, 28, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 10, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 28, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 96, 96, 96, 96] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 281 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113433 none CC1=C(C)CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 8, 22, 22, 22, 96, 96, 96, 159, 201, 201, 201, 201, 201, 96, 96, 22, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 8, 22, 22, 22, 22, 96, 159, 159, 201, 201, 22, 22, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 34, 48, 49, 50, 35, 25, 26, 51] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 746 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113433 none CC1=C(C)CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 88, 88, 88, 45, 45, 45, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 45, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 88, 45, 45, 45, 45, 12, 6, 6, 4, 4, 45, 45, 201, 201, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 584 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113433 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113433 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113433/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113433/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113433 Building REAL300020113434 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113434' /scratch/stefan/7770410/working/building/REAL300020113434 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113434 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113434/0 /scratch/stefan/7770410/working/building/REAL300020113434 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/470 `/scratch/stefan/7770410/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)CCCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113434.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113434 none CC(C)(C)CCCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 88, 110, 110, 110, 88, 87, 17, 17, 17, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 110, 110, 110, 110, 110, 110, 110, 110, 110, 110, 110, 110, 110, 110, 110, 87, 87, 17, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [17, 13, 14, 15, 16, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55]) total number of confs: 744 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113434 none CC(C)(C)CCCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 171, 201, 201, 201, 171, 188, 50, 50, 50, 33, 33, 33, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 33, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 188, 188, 50, 33, 33, 33, 33, 8, 4, 4, 2, 2, 33, 33] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 1158 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113434 none CC(C)(C)CCCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 28, 34, 34, 34, 28, 20, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 20, 31, 31, 31, 31, 31, 7, 7, 1, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 20, 20, 5, 1, 1, 1, 1, 7, 20, 20, 31, 31, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 46, 45, 48, 14, 54, 55, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53]) total number of confs: 344 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113434 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113434/1 /scratch/stefan/7770410/working/building/REAL300020113434 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 471) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/471 `/scratch/stefan/7770410/working/3D/471' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)CCCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113434.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113434/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113434 none CC(C)(C)CCCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 89, 111, 111, 111, 89, 88, 17, 17, 17, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 111, 111, 111, 111, 111, 111, 111, 111, 111, 111, 111, 111, 111, 111, 111, 88, 88, 17, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [17, 13, 14, 15, 16, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55]) total number of confs: 747 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113434 none CC(C)(C)CCCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 171, 201, 201, 201, 171, 188, 50, 50, 50, 33, 33, 33, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 33, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 188, 188, 50, 33, 33, 33, 33, 8, 4, 4, 2, 2, 33, 33] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 1158 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113434 none CC(C)(C)CCCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 28, 34, 34, 34, 28, 20, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 20, 31, 31, 31, 31, 31, 7, 7, 1, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 20, 20, 5, 1, 1, 1, 1, 7, 20, 20, 31, 31, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 46, 45, 48, 14, 54, 55, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53]) total number of confs: 344 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113434 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113434 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113434/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113434/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113434 Building REAL300020113435 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113435' /scratch/stefan/7770410/working/building/REAL300020113435 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113435 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113435/0 /scratch/stefan/7770410/working/building/REAL300020113435 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/472 `/scratch/stefan/7770410/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1CCCC2) `REAL300020113435.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113435 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 55, 135, 135, 135, 135, 135, 135, 135, 135, 135, 55, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 135, 135, 135, 135, 135, 135, 135, 135, 135, 135, 135] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 288 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113435 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 44, 44, 44, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 44, 112, 201, 201, 201, 201, 201, 201, 201, 201, 201, 112, 44, 44, 44, 44, 8, 4, 4, 2, 2, 44, 44, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 443 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113435 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 34, 44, 44, 44, 44, 44, 13, 13, 1, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 13, 34, 34, 44, 44, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113435 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 24, 24, 24, 135, 135, 135, 177, 201, 201, 201, 201, 201, 135, 135, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 24, 24, 24, 24, 135, 177, 177, 201, 201, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 565 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113435 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113435/1 /scratch/stefan/7770410/working/building/REAL300020113435 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 473) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/473 `/scratch/stefan/7770410/working/3D/473' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1CCCC2) `REAL300020113435.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113435 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 55, 136, 136, 136, 136, 136, 136, 136, 136, 136, 55, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 136, 136, 136, 136, 136, 136, 136, 136, 136, 136, 136] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 289 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113435 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 44, 44, 44, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 44, 112, 201, 201, 201, 201, 201, 201, 201, 201, 201, 112, 44, 44, 44, 44, 8, 4, 4, 2, 2, 44, 44, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 442 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113435 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 34, 44, 44, 44, 44, 44, 13, 13, 1, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 13, 34, 34, 44, 44, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113435 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 24, 24, 24, 136, 136, 136, 177, 201, 201, 201, 201, 201, 136, 136, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 24, 24, 24, 24, 136, 177, 177, 201, 201, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 560 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113435 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113435 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113435/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113435/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113435 Building REAL300020113436 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113436' /scratch/stefan/7770410/working/building/REAL300020113436 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113436 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113436/0 /scratch/stefan/7770410/working/building/REAL300020113436 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/474 `/scratch/stefan/7770410/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C2=CC=CC=C2O1) `REAL300020113436.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113436 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 33, 46, 47, 47, 47, 47, 11, 11, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 1, 1, 1, 1, 11, 33, 33, 46, 46, 1, 1, 18, 18, 18, 18] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 42, 43, 21] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 206 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113436 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 31, 31, 31, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 31, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 96, 96, 96, 96] 201 rigid atoms, others: [37, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 195 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113436 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 18, 18, 18, 96, 96, 96, 166, 201, 201, 201, 201, 201, 96, 96, 18, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 18, 18, 18, 18, 96, 166, 166, 201, 201, 18, 18, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 45, 46, 47, 22, 23, 24, 25, 26, 27, 28] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 739 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113436 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 101, 101, 101, 47, 47, 47, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 47, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 101, 47, 47, 47, 47, 9, 5, 5, 3, 3, 47, 47, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 443 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113436 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113436/1 /scratch/stefan/7770410/working/building/REAL300020113436 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 475) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/475 `/scratch/stefan/7770410/working/3D/475' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C2=CC=CC=C2O1) `REAL300020113436.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113436/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113436 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 33, 46, 47, 47, 47, 47, 11, 11, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 1, 1, 1, 1, 11, 33, 33, 46, 46, 1, 1, 18, 18, 18, 18] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 42, 43, 21] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 206 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113436 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 31, 31, 31, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 31, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 96, 96, 96, 96] 201 rigid atoms, others: [37, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 195 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113436 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 18, 18, 18, 96, 96, 96, 166, 201, 201, 201, 201, 201, 96, 96, 18, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 18, 18, 18, 18, 96, 166, 166, 201, 201, 18, 18, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 45, 46, 47, 22, 23, 24, 25, 26, 27, 28] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 739 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113436 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 101, 101, 101, 47, 47, 47, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 47, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 101, 47, 47, 47, 47, 9, 5, 5, 3, 3, 47, 47, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 444 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113436 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113436 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113436/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113436/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113436 Building REAL300020113437 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113437' /scratch/stefan/7770410/working/building/REAL300020113437 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113437 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113437/0 /scratch/stefan/7770410/working/building/REAL300020113437 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/476 `/scratch/stefan/7770410/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CSC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1Cl) `REAL300020113437.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113437 none CC1=CSC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 37, 50, 70, 70, 70, 70, 8, 8, 1, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 8, 37, 37, 50, 50, 1, 1] 181 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 40, 41, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) total number of confs: 269 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113437 none CC1=CSC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 77, 25, 25, 25, 8, 8, 8, 1, 1, 1, 1, 1, 8, 13, 20, 20, 20, 20, 1, 1, 8, 77, 77, 77, 77, 77, 77, 25, 8, 8, 8, 8, 1, 8, 8, 13, 13, 8, 8] 181 rigid atoms, others: [35, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 202 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113437 none CC1=CSC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 26, 26, 26, 77, 77, 77, 156, 181, 181, 181, 181, 181, 77, 77, 26, 1, 1, 2, 2, 2, 1, 7, 26, 26, 26, 26, 77, 156, 156, 181, 181, 26, 26] 181 rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 25, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 666 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113437 none CC1=CSC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [181, 181, 181, 181, 122, 122, 122, 72, 72, 72, 23, 23, 23, 7, 4, 1, 1, 1, 1, 1, 1, 23, 23, 72, 181, 181, 181, 181, 181, 181, 122, 72, 72, 72, 72, 23, 7, 7, 4, 4, 72, 72] 181 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 438 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113437 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113437/1 /scratch/stefan/7770410/working/building/REAL300020113437 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 477) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/477 `/scratch/stefan/7770410/working/3D/477' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CSC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1Cl) `REAL300020113437.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113437/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113437 none CC1=CSC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 38, 51, 71, 71, 71, 71, 8, 8, 1, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 8, 38, 38, 51, 51, 1, 1] 182 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 40, 41, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) total number of confs: 272 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113437 none CC1=CSC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 78, 25, 25, 25, 8, 8, 8, 1, 1, 1, 1, 1, 8, 13, 20, 20, 20, 20, 1, 1, 8, 78, 78, 78, 78, 78, 78, 25, 8, 8, 8, 8, 1, 8, 8, 13, 13, 8, 8] 182 rigid atoms, others: [35, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 204 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113437 none CC1=CSC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 26, 26, 26, 78, 78, 78, 157, 182, 182, 182, 182, 182, 78, 78, 26, 1, 1, 2, 2, 2, 1, 7, 26, 26, 26, 26, 78, 157, 157, 182, 182, 26, 26] 182 rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 25, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 667 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113437 none CC1=CSC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [181, 181, 181, 181, 122, 122, 122, 72, 72, 72, 23, 23, 23, 7, 4, 1, 1, 1, 1, 1, 1, 23, 23, 72, 181, 181, 181, 181, 181, 181, 122, 72, 72, 72, 72, 23, 7, 7, 4, 4, 72, 72] 181 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 438 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113437 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113437 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113437/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113437/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113437 Building REAL300020113438 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113438' /scratch/stefan/7770410/working/building/REAL300020113438 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113438 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113438/0 /scratch/stefan/7770410/working/building/REAL300020113438 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/478 `/scratch/stefan/7770410/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NSC2=CC=CC=C21) `REAL300020113438.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113438 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NSC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 14, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 18, 18, 18, 18, 1, 1, 12, 52, 100, 100, 100, 100, 100, 100, 100, 100, 52, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 100, 100, 100, 100] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 260 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113438 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NSC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 14, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [193, 193, 100, 100, 100, 19, 19, 19, 6, 4, 1, 1, 1, 1, 1, 1, 19, 19, 100, 193, 201, 201, 201, 201, 201, 201, 201, 201, 193, 100, 100, 100, 100, 19, 6, 6, 4, 4, 100, 100, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 549 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113438 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NSC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 14, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 59, 79, 100, 100, 100, 100, 12, 12, 1, 6, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 12, 59, 59, 79, 79, 1, 1, 17, 17, 17, 17] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 376 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113438 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NSC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 14, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 17, 17, 17, 100, 100, 100, 167, 201, 201, 201, 201, 201, 100, 100, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 17, 100, 167, 167, 201, 201, 17, 17, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 688 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113438 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113438/1 /scratch/stefan/7770410/working/building/REAL300020113438 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 479) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/479 `/scratch/stefan/7770410/working/3D/479' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NSC2=CC=CC=C21) `REAL300020113438.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113438 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NSC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 14, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 18, 18, 18, 18, 1, 1, 12, 53, 100, 100, 100, 100, 100, 100, 100, 100, 53, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 100, 100, 100, 100] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 258 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113438 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NSC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 14, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [193, 193, 103, 103, 103, 20, 20, 20, 6, 4, 1, 1, 1, 1, 1, 1, 20, 20, 103, 193, 201, 201, 201, 201, 201, 201, 201, 201, 193, 103, 103, 103, 103, 20, 6, 6, 4, 4, 103, 103, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 544 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113438 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NSC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 14, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 62, 82, 102, 102, 102, 102, 12, 12, 1, 6, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 12, 62, 62, 82, 82, 1, 1, 17, 17, 17, 17] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 383 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113438 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NSC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 14, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 17, 17, 17, 100, 100, 100, 166, 201, 201, 201, 201, 201, 100, 100, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 17, 100, 166, 166, 201, 201, 17, 17, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 689 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113438 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113438 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113438/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113438/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113438 Building REAL300020113439 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113439' /scratch/stefan/7770410/working/building/REAL300020113439 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113439 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113439/0 /scratch/stefan/7770410/working/building/REAL300020113439 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/480 `/scratch/stefan/7770410/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(CC=C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113439.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113439 none C=CCC(CC=C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 78, 51, 21, 51, 76, 105, 21, 21, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 104, 104, 104, 78, 78, 51, 76, 76, 105, 105, 105, 21, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 732 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113439 none C=CCC(CC=C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [192, 165, 131, 58, 131, 163, 193, 58, 58, 34, 34, 34, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 34, 192, 192, 192, 165, 165, 131, 163, 163, 193, 193, 193, 58, 34, 34, 34, 34, 7, 4, 4, 2, 2, 34, 34] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 1137 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113439 none C=CCC(CC=C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 21, 13, 6, 13, 19, 31, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 21, 34, 34, 34, 34, 34, 8, 8, 1, 33, 33, 33, 21, 21, 13, 19, 19, 31, 31, 31, 6, 1, 1, 1, 1, 8, 21, 21, 34, 34, 1, 1] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 348 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113439 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113439/1 /scratch/stefan/7770410/working/building/REAL300020113439 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 481) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/481 `/scratch/stefan/7770410/working/3D/481' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(CC=C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113439.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113439/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113439 none C=CCC(CC=C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 77, 50, 20, 50, 75, 104, 20, 20, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 103, 103, 103, 77, 77, 50, 75, 75, 104, 104, 104, 20, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 730 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113439 none C=CCC(CC=C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [192, 165, 132, 57, 132, 163, 193, 57, 57, 34, 34, 34, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 34, 192, 192, 192, 165, 165, 132, 163, 163, 193, 193, 193, 57, 34, 34, 34, 34, 7, 4, 4, 2, 2, 34, 34] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 1132 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113439 none C=CCC(CC=C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 21, 13, 6, 13, 19, 31, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 21, 34, 34, 34, 34, 34, 8, 8, 1, 33, 33, 33, 21, 21, 13, 19, 19, 31, 31, 31, 6, 1, 1, 1, 1, 8, 21, 21, 34, 34, 1, 1] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 348 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113439 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113439 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113439/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113439/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113439 Building REAL300020113440 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113440' /scratch/stefan/7770410/working/building/REAL300020113440 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113440 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113440/0 /scratch/stefan/7770410/working/building/REAL300020113440 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/482 `/scratch/stefan/7770410/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC=CCC1) `REAL300020113440.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113440 none CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 36, 51, 51, 51, 51, 51, 13, 13, 1, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 36, 36, 51, 51, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16] 201 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 39, 40, 20, 30, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 245 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113440 none CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 45, 45, 45, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 118, 118, 118, 118, 118, 118, 118, 118, 45, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 118, 118, 118, 118, 118, 118, 118, 118] 201 rigid atoms, others: [34, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 367 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113440 none CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 4, 4, 4, 16, 16, 16, 118, 118, 118, 176, 201, 201, 201, 201, 201, 118, 118, 16, 1, 1, 1, 1, 1, 2, 2, 2, 4, 16, 16, 16, 16, 118, 176, 176, 201, 201, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 41, 42, 43, 44, 45, 46, 47, 48, 21, 22, 23, 24, 25] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 630 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113440 none CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 103, 103, 103, 54, 54, 54, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 54, 201, 201, 201, 201, 201, 201, 201, 201, 103, 54, 54, 54, 54, 9, 4, 4, 2, 2, 54, 54, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 609 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113440 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113440/1 /scratch/stefan/7770410/working/building/REAL300020113440 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 483) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/483 `/scratch/stefan/7770410/working/3D/483' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC=CCC1) `REAL300020113440.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113440/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113440 none CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 36, 51, 51, 51, 51, 51, 13, 13, 1, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 36, 36, 51, 51, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16] 201 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 39, 40, 20, 30, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 245 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113440 none CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 45, 45, 45, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 118, 118, 118, 118, 118, 118, 118, 118, 45, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 118, 118, 118, 118, 118, 118, 118, 118] 201 rigid atoms, others: [34, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 367 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113440 none CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 4, 4, 4, 16, 16, 16, 118, 118, 118, 176, 201, 201, 201, 201, 201, 118, 118, 16, 1, 1, 1, 1, 1, 2, 2, 2, 4, 16, 16, 16, 16, 118, 176, 176, 201, 201, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 41, 42, 43, 44, 45, 46, 47, 48, 21, 22, 23, 24, 25] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 624 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113440 none CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 102, 102, 102, 53, 53, 53, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 53, 201, 201, 201, 201, 201, 201, 201, 201, 102, 53, 53, 53, 53, 9, 4, 4, 2, 2, 53, 53, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 605 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113440 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113440 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113440/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113440/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113440 Building REAL300020113441 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113441' /scratch/stefan/7770410/working/building/REAL300020113441 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113441 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113441/0 /scratch/stefan/7770410/working/building/REAL300020113441 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/484 `/scratch/stefan/7770410/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1) `REAL300020113441.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113441 none CN1C=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 39, 57, 65, 65, 65, 65, 13, 13, 1, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 13, 39, 39, 57, 57, 1, 1] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 40, 41, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) total number of confs: 268 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113441 none CN1C=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 91, 91, 49, 49, 49, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 91, 91, 91, 91, 91, 49, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [35, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 237 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113441 none CN1C=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 91, 91, 91, 166, 201, 201, 201, 201, 201, 91, 91, 11, 1, 2, 2, 2, 1, 3, 11, 11, 11, 11, 91, 166, 166, 201, 201, 11, 11] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 723 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113441 none CN1C=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 141, 141, 141, 66, 66, 66, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 66, 201, 201, 201, 201, 201, 141, 66, 66, 66, 66, 11, 6, 6, 4, 4, 66, 66] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 523 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113441 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113441/1 /scratch/stefan/7770410/working/building/REAL300020113441 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 485) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/485 `/scratch/stefan/7770410/working/3D/485' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1) `REAL300020113441.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113441 none CN1C=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 39, 57, 65, 65, 65, 65, 13, 13, 1, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 13, 39, 39, 57, 57, 1, 1] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 40, 41, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) total number of confs: 268 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113441 none CN1C=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 91, 91, 49, 49, 49, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 91, 91, 91, 91, 91, 49, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [35, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 237 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113441 none CN1C=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 91, 91, 91, 166, 201, 201, 201, 201, 201, 91, 91, 11, 1, 2, 2, 2, 1, 3, 11, 11, 11, 11, 91, 166, 166, 201, 201, 11, 11] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 723 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113441 none CN1C=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 138, 138, 138, 65, 65, 65, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 65, 201, 201, 201, 201, 201, 138, 65, 65, 65, 65, 10, 6, 6, 4, 4, 65, 65] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 519 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113441 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113441 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113441/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113441/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113441 Building REAL300020113442 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113442' /scratch/stefan/7770410/working/building/REAL300020113442 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113442 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113442/0 /scratch/stefan/7770410/working/building/REAL300020113442 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/486 `/scratch/stefan/7770410/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CS(=O)(=O)C1) `REAL300020113442.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113442 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 14, 11, 11, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 12, 12, 12, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 12, 33, 105, 105, 105, 105, 105, 33, 12, 12, 12, 12, 1, 8, 8, 10, 10, 12, 12, 105, 105, 105, 105, 105] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 315 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113442 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 14, 11, 11, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 57, 57, 57, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 57, 104, 201, 201, 201, 201, 201, 104, 57, 57, 57, 57, 12, 6, 6, 4, 4, 57, 57, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 600 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113442 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 14, 11, 11, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 36, 51, 57, 57, 57, 57, 12, 12, 1, 6, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 12, 36, 36, 51, 51, 1, 1, 29, 29, 29, 29, 29] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 35, 36, 26, 27, 28, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41]) total number of confs: 280 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113442 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 14, 11, 11, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 29, 29, 29, 105, 105, 105, 163, 201, 201, 201, 201, 201, 105, 105, 29, 1, 1, 1, 1, 1, 1, 11, 29, 29, 29, 29, 105, 163, 163, 201, 201, 29, 29, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 37, 38, 39, 40, 41, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 706 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113442 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113442/1 /scratch/stefan/7770410/working/building/REAL300020113442 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 487) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/487 `/scratch/stefan/7770410/working/3D/487' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CS(=O)(=O)C1) `REAL300020113442.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113442 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 14, 11, 11, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 12, 12, 12, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 12, 33, 105, 105, 105, 105, 105, 33, 12, 12, 12, 12, 1, 8, 8, 10, 10, 12, 12, 105, 105, 105, 105, 105] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 315 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113442 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 14, 11, 11, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 57, 57, 57, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 57, 104, 201, 201, 201, 201, 201, 104, 57, 57, 57, 57, 12, 6, 6, 4, 4, 57, 57, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 600 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113442 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 14, 11, 11, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 36, 51, 57, 57, 57, 57, 12, 12, 1, 6, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 12, 36, 36, 51, 51, 1, 1, 29, 29, 29, 29, 29] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 35, 36, 26, 27, 28, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41]) total number of confs: 280 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113442 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 14, 11, 11, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 29, 29, 29, 105, 105, 105, 163, 201, 201, 201, 201, 201, 105, 105, 29, 1, 1, 1, 1, 1, 1, 11, 29, 29, 29, 29, 105, 163, 163, 201, 201, 29, 29, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 37, 38, 39, 40, 41, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 706 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113442 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113442 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113442/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113442/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113442 Building REAL300020113443 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113443' /scratch/stefan/7770410/working/building/REAL300020113443 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113443 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113443/0 /scratch/stefan/7770410/working/building/REAL300020113443 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/488 `/scratch/stefan/7770410/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CS1) `REAL300020113443.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113443 none CC1=C(C)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 22, 35, 35, 35, 35, 35, 8, 8, 1, 16, 16, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 8, 22, 22, 35, 35, 1, 1, 16] 201 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 173 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113443 none CC1=C(C)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 79, 27, 27, 27, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 79, 79, 79, 79, 79, 79, 79, 79, 27, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8, 79] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 161 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113443 none CC1=C(C)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 16, 16, 16, 79, 79, 79, 144, 201, 201, 201, 201, 201, 79, 79, 16, 1, 1, 2, 2, 2, 2, 2, 2, 8, 16, 16, 16, 16, 79, 144, 144, 201, 201, 16, 16, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 821 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113443 none CC1=C(C)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 82, 82, 82, 36, 36, 36, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 36, 201, 201, 201, 201, 201, 201, 201, 201, 82, 36, 36, 36, 36, 8, 4, 4, 2, 2, 36, 36, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 402 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113443 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113443/1 /scratch/stefan/7770410/working/building/REAL300020113443 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 489) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/489 `/scratch/stefan/7770410/working/3D/489' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CS1) `REAL300020113443.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113443/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113443 none CC1=C(C)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 22, 35, 35, 35, 35, 35, 8, 8, 1, 16, 16, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 8, 22, 22, 35, 35, 1, 1, 16] 201 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 173 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113443 none CC1=C(C)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 78, 27, 27, 27, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 78, 78, 78, 78, 78, 78, 78, 78, 27, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8, 78] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 160 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113443 none CC1=C(C)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 16, 16, 16, 78, 78, 78, 143, 201, 201, 201, 201, 201, 78, 78, 16, 1, 1, 2, 2, 2, 2, 2, 2, 8, 16, 16, 16, 16, 78, 143, 143, 201, 201, 16, 16, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 826 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113443 none CC1=C(C)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 82, 82, 82, 37, 37, 37, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 37, 201, 201, 201, 201, 201, 201, 201, 201, 82, 37, 37, 37, 37, 9, 4, 4, 2, 2, 37, 37, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 401 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113443 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113443 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113443/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113443/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113443 Building REAL300020113444 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113444' /scratch/stefan/7770410/working/building/REAL300020113444 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113444 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113444/0 /scratch/stefan/7770410/working/building/REAL300020113444 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/490 `/scratch/stefan/7770410/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=CC(Cl)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113444.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113444 none CCN1N=CC(Cl)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [39, 22, 22, 22, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 23, 31, 32, 32, 32, 32, 6, 6, 1, 39, 39, 39, 39, 39, 22, 6, 1, 1, 1, 1, 6, 23, 23, 31, 31, 1, 1] 123 rigid atoms, others: [34, 35, 36, 37, 44, 10, 11, 12, 13, 14, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 249 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113444 none CCN1N=CC(Cl)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [67, 48, 48, 48, 48, 48, 48, 23, 23, 23, 6, 6, 6, 1, 1, 1, 1, 1, 8, 10, 11, 11, 11, 11, 1, 1, 6, 67, 67, 67, 67, 67, 48, 23, 6, 6, 6, 6, 1, 8, 8, 10, 10, 6, 6] 123 rigid atoms, others: [38, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 241 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113444 none CCN1N=CC(Cl)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 22, 22, 22, 48, 48, 48, 78, 95, 96, 96, 96, 96, 48, 48, 22, 5, 5, 5, 5, 5, 1, 7, 22, 22, 22, 22, 48, 78, 78, 95, 95, 22, 22] 123 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 357 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113444 none CCN1N=CC(Cl)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [147, 116, 116, 116, 116, 116, 116, 91, 91, 91, 41, 41, 41, 15, 15, 15, 7, 4, 1, 1, 1, 1, 1, 1, 15, 15, 41, 147, 147, 147, 147, 147, 116, 91, 41, 41, 41, 41, 15, 7, 7, 4, 4, 41, 41] 147 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 484 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113444 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113444/1 /scratch/stefan/7770410/working/building/REAL300020113444 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 491) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/491 `/scratch/stefan/7770410/working/3D/491' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=CC(Cl)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113444.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113444/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113444 none CCN1N=CC(Cl)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [39, 22, 22, 22, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 23, 31, 32, 32, 32, 32, 6, 6, 1, 39, 39, 39, 39, 39, 22, 6, 1, 1, 1, 1, 6, 23, 23, 31, 31, 1, 1] 123 rigid atoms, others: [34, 35, 36, 37, 44, 10, 11, 12, 13, 14, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 249 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113444 none CCN1N=CC(Cl)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [67, 48, 48, 48, 48, 48, 48, 23, 23, 23, 6, 6, 6, 1, 1, 1, 1, 1, 8, 10, 11, 11, 11, 11, 1, 1, 6, 67, 67, 67, 67, 67, 48, 23, 6, 6, 6, 6, 1, 8, 8, 10, 10, 6, 6] 123 rigid atoms, others: [38, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 241 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113444 none CCN1N=CC(Cl)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 22, 22, 22, 48, 48, 48, 78, 95, 96, 96, 96, 96, 48, 48, 22, 5, 5, 5, 5, 5, 1, 7, 22, 22, 22, 22, 48, 78, 78, 95, 95, 22, 22] 123 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 357 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113444 none CCN1N=CC(Cl)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [147, 116, 116, 116, 116, 116, 116, 91, 91, 91, 41, 41, 41, 15, 15, 15, 7, 4, 1, 1, 1, 1, 1, 1, 15, 15, 41, 147, 147, 147, 147, 147, 116, 91, 41, 41, 41, 41, 15, 7, 7, 4, 4, 41, 41] 147 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 484 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113444 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113444 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113444/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113444/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113444 Building REAL300020113445 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113445' /scratch/stefan/7770410/working/building/REAL300020113445 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113445 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113445/0 /scratch/stefan/7770410/working/building/REAL300020113445 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/492 `/scratch/stefan/7770410/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113445.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113445 none CCC(C)(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 98, 44, 98, 98, 14, 14, 14, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 104, 104, 104, 104, 104, 98, 98, 98, 98, 98, 98, 44, 44, 14, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [11, 43, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 464 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113445 none CCC(C)(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 106, 201, 201, 47, 47, 47, 32, 32, 32, 8, 8, 8, 5, 2, 1, 1, 1, 1, 1, 1, 8, 8, 32, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 106, 106, 47, 32, 32, 32, 32, 8, 5, 5, 2, 2, 32, 32] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 864 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113445 none CCC(C)(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 21, 10, 21, 21, 4, 4, 4, 1, 1, 1, 1, 1, 7, 7, 7, 20, 32, 32, 32, 32, 32, 7, 7, 1, 27, 27, 27, 27, 27, 21, 21, 21, 21, 21, 21, 10, 10, 4, 1, 1, 1, 1, 7, 20, 20, 32, 32, 1, 1] 201 rigid atoms, others: [49, 39, 8, 9, 10, 11, 12, 48, 40, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113445 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113445/1 /scratch/stefan/7770410/working/building/REAL300020113445 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 493) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/493 `/scratch/stefan/7770410/working/3D/493' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113445.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113445 none CCC(C)(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 100, 46, 100, 100, 15, 15, 15, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 104, 104, 104, 104, 104, 100, 100, 100, 100, 100, 100, 46, 46, 15, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [11, 43, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 457 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113445 none CCC(C)(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 106, 201, 201, 46, 46, 46, 31, 31, 31, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 31, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 106, 106, 46, 31, 31, 31, 31, 7, 4, 4, 2, 2, 31, 31] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 858 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113445 none CCC(C)(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 22, 11, 22, 22, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 18, 30, 30, 30, 30, 30, 7, 7, 1, 27, 27, 27, 27, 27, 22, 22, 22, 22, 22, 22, 11, 11, 5, 1, 1, 1, 1, 7, 18, 18, 30, 30, 1, 1] 201 rigid atoms, others: [49, 39, 8, 9, 10, 11, 12, 48, 40, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113445 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113445 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113445/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113445/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113445 Building REAL300020113446 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113446' /scratch/stefan/7770410/working/building/REAL300020113446 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113446 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113446/0 /scratch/stefan/7770410/working/building/REAL300020113446 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/494 `/scratch/stefan/7770410/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)CCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113446.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113446 none CCCC(C)CCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 134, 81, 134, 76, 69, 13, 13, 13, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 139, 139, 139, 139, 139, 139, 139, 134, 134, 134, 134, 81, 81, 81, 81, 69, 69, 13, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [17, 13, 14, 15, 16, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55]) total number of confs: 716 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113446 none CCCC(C)CCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 130, 201, 123, 117, 28, 28, 28, 25, 25, 25, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 25, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 130, 130, 130, 130, 117, 117, 28, 25, 25, 25, 25, 8, 4, 4, 2, 2, 25, 25] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 948 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113446 none CCCC(C)CCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 47, 26, 47, 22, 18, 3, 3, 3, 1, 1, 1, 1, 1, 7, 7, 7, 15, 23, 23, 23, 23, 23, 7, 7, 1, 53, 53, 53, 53, 53, 53, 53, 47, 47, 47, 47, 26, 26, 26, 26, 18, 18, 3, 1, 1, 1, 1, 7, 15, 15, 23, 23, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 46, 45, 48, 14, 54, 55, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53]) total number of confs: 385 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113446 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113446/1 /scratch/stefan/7770410/working/building/REAL300020113446 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 495) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/495 `/scratch/stefan/7770410/working/3D/495' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)CCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113446.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113446 none CCCC(C)CCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 135, 82, 135, 77, 70, 13, 13, 13, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 139, 139, 139, 139, 139, 139, 139, 135, 135, 135, 135, 82, 82, 82, 82, 70, 70, 13, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [17, 13, 14, 15, 16, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55]) total number of confs: 713 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113446 none CCCC(C)CCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 130, 201, 122, 117, 27, 27, 27, 24, 24, 24, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 24, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 130, 130, 130, 130, 117, 117, 27, 24, 24, 24, 24, 7, 4, 4, 2, 2, 24, 24] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 953 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113446 none CCCC(C)CCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 47, 26, 47, 22, 18, 3, 3, 3, 1, 1, 1, 1, 1, 7, 7, 7, 15, 23, 23, 23, 23, 23, 7, 7, 1, 52, 52, 52, 52, 52, 52, 52, 47, 47, 47, 47, 26, 26, 26, 26, 18, 18, 3, 1, 1, 1, 1, 7, 15, 15, 23, 23, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 46, 45, 48, 14, 54, 55, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53]) total number of confs: 379 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113446 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113446 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113446/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113446/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113446 Building REAL300020113447 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113447' /scratch/stefan/7770410/working/building/REAL300020113447 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113447 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113447/0 /scratch/stefan/7770410/working/building/REAL300020113447 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/496 `/scratch/stefan/7770410/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)CCCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113447.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113447 none CCC(C)CCCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [123, 123, 60, 123, 66, 60, 59, 14, 14, 14, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 123, 123, 123, 123, 123, 123, 123, 123, 123, 66, 66, 66, 66, 66, 66, 59, 59, 14, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [17, 13, 14, 15, 16, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55]) total number of confs: 668 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113447 none CCC(C)CCCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 102, 201, 111, 102, 110, 34, 34, 34, 27, 27, 27, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 27, 201, 201, 201, 201, 201, 201, 201, 201, 201, 111, 111, 111, 111, 111, 111, 110, 110, 34, 27, 27, 27, 27, 7, 4, 4, 2, 2, 27, 27] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 1025 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113447 none CCC(C)CCCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 17, 39, 21, 17, 16, 4, 4, 4, 1, 1, 1, 1, 1, 7, 7, 7, 17, 27, 27, 27, 27, 27, 7, 7, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39, 21, 21, 21, 21, 21, 21, 16, 16, 4, 1, 1, 1, 1, 7, 17, 17, 27, 27, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 46, 45, 48, 14, 54, 55, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53]) total number of confs: 331 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113447 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113447/1 /scratch/stefan/7770410/working/building/REAL300020113447 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 497) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/497 `/scratch/stefan/7770410/working/3D/497' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)CCCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113447.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113447/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113447 none CCC(C)CCCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 60, 125, 67, 60, 59, 14, 14, 14, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 125, 125, 125, 125, 125, 125, 125, 125, 125, 67, 67, 67, 67, 67, 67, 59, 59, 14, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [17, 13, 14, 15, 16, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55]) total number of confs: 692 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113447 none CCC(C)CCCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 101, 201, 110, 101, 109, 34, 34, 34, 27, 27, 27, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 27, 201, 201, 201, 201, 201, 201, 201, 201, 201, 110, 110, 110, 110, 110, 110, 109, 109, 34, 27, 27, 27, 27, 7, 4, 4, 2, 2, 27, 27] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 1028 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113447 none CCC(C)CCCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 17, 40, 21, 17, 16, 4, 4, 4, 1, 1, 1, 1, 1, 7, 7, 7, 17, 27, 27, 27, 27, 27, 7, 7, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 21, 21, 21, 21, 21, 21, 16, 16, 4, 1, 1, 1, 1, 7, 17, 17, 27, 27, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 46, 45, 48, 14, 54, 55, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53]) total number of confs: 337 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113447 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113447 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113447/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113447/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113447 Building REAL300020113448 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113448' /scratch/stefan/7770410/working/building/REAL300020113448 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113448 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113448/0 /scratch/stefan/7770410/working/building/REAL300020113448 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/498 `/scratch/stefan/7770410/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C)(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113448.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113448 none CC(C)C(C)(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 42, 82, 82, 42, 42, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 42, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11] 201 rigid atoms, others: [11, 43, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 373 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113448 none CC(C)C(C)(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 177, 201, 100, 177, 177, 100, 100, 65, 65, 65, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 65, 201, 201, 201, 201, 201, 201, 201, 177, 177, 177, 177, 177, 177, 100, 65, 65, 65, 65, 13, 6, 6, 4, 4, 65, 65] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 811 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113448 none CC(C)C(C)(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 6, 15, 15, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 41, 59, 70, 70, 70, 70, 11, 11, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 11, 41, 41, 59, 59, 1, 1] 201 rigid atoms, others: [49, 39, 8, 9, 10, 11, 12, 48, 40, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113448 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113448/1 /scratch/stefan/7770410/working/building/REAL300020113448 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 499) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/499 `/scratch/stefan/7770410/working/3D/499' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C)(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113448.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113448/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113448 none CC(C)C(C)(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 42, 82, 82, 42, 42, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 42, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11] 201 rigid atoms, others: [11, 43, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 373 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113448 none CC(C)C(C)(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 177, 201, 100, 177, 177, 100, 100, 65, 65, 65, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 65, 201, 201, 201, 201, 201, 201, 201, 177, 177, 177, 177, 177, 177, 100, 65, 65, 65, 65, 13, 6, 6, 4, 4, 65, 65] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 811 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113448 none CC(C)C(C)(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 6, 15, 15, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 41, 59, 70, 70, 70, 70, 11, 11, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 11, 41, 41, 59, 59, 1, 1] 201 rigid atoms, others: [49, 39, 8, 9, 10, 11, 12, 48, 40, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113448 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113448 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113448/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113448/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113448 Building REAL300020113449 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113449' /scratch/stefan/7770410/working/building/REAL300020113449 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113449 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113449/0 /scratch/stefan/7770410/working/building/REAL300020113449 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/500 `/scratch/stefan/7770410/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=C1) `REAL300020113449.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113449 none COC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 29, 19, 29, 29, 19, 3, 3, 3, 1, 1, 1, 1, 1, 7, 7, 7, 20, 31, 31, 31, 31, 31, 7, 7, 1, 29, 29, 29, 45, 45, 45, 29, 29, 19, 19, 3, 1, 1, 1, 1, 7, 20, 20, 31, 31, 1, 1, 29, 29, 29, 29] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 293 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113449 none COC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 105, 71, 105, 105, 71, 13, 13, 13, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 105, 105, 105, 133, 133, 133, 105, 105, 71, 71, 13, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 105, 105, 105, 105] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 570 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113449 none COC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 5, 17, 17, 17, 29, 29, 29, 105, 105, 105, 166, 201, 201, 201, 201, 201, 105, 105, 29, 1, 1, 1, 3, 3, 3, 1, 1, 5, 5, 17, 29, 29, 29, 29, 105, 166, 166, 201, 201, 29, 29, 2, 2, 2, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 51, 26, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 718 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113449 none COC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 142, 201, 201, 142, 40, 40, 40, 31, 31, 31, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 31, 201, 201, 201, 201, 201, 201, 201, 201, 142, 142, 40, 31, 31, 31, 31, 7, 4, 4, 2, 2, 31, 31, 201, 201, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 928 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113449 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113449/1 /scratch/stefan/7770410/working/building/REAL300020113449 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 501) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/501 `/scratch/stefan/7770410/working/3D/501' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=C1) `REAL300020113449.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113449/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113449 none COC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 30, 19, 30, 30, 19, 3, 3, 3, 1, 1, 1, 1, 1, 7, 7, 7, 20, 31, 31, 31, 31, 31, 7, 7, 1, 30, 30, 30, 47, 47, 47, 30, 30, 19, 19, 3, 1, 1, 1, 1, 7, 20, 20, 31, 31, 1, 1, 30, 30, 30, 30] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 302 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113449 none COC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 105, 71, 105, 105, 71, 13, 13, 13, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 105, 105, 105, 133, 133, 133, 105, 105, 71, 71, 13, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 105, 105, 105, 105] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 570 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113449 none COC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 5, 18, 18, 18, 30, 30, 30, 105, 105, 105, 166, 201, 201, 201, 201, 201, 105, 105, 30, 1, 1, 1, 3, 3, 3, 1, 1, 5, 5, 18, 30, 30, 30, 30, 105, 166, 166, 201, 201, 30, 30, 2, 2, 2, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 51, 26, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 716 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113449 none COC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 143, 201, 201, 143, 42, 42, 42, 31, 31, 31, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 31, 201, 201, 201, 201, 201, 201, 201, 201, 143, 143, 42, 31, 31, 31, 31, 7, 4, 4, 2, 2, 31, 31, 201, 201, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 926 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113449 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113449 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113449/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113449/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113449 Building REAL300020113450 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113450' /scratch/stefan/7770410/working/building/REAL300020113450 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113450 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113450/0 /scratch/stefan/7770410/working/building/REAL300020113450 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/502 `/scratch/stefan/7770410/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1) `REAL300020113450.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113450 none CC1=NN(CC(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 23, 12, 6, 12, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 32, 44, 49, 49, 49, 49, 8, 8, 1, 35, 35, 35, 35, 35, 23, 23, 12, 12, 12, 12, 6, 1, 1, 1, 1, 8, 32, 32, 44, 44, 1, 1, 35, 35] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50]) total number of confs: 300 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113450 none CC1=NN(CC(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 81, 45, 22, 45, 22, 22, 8, 8, 8, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 8, 103, 103, 103, 103, 103, 81, 81, 45, 45, 45, 45, 22, 8, 8, 8, 8, 1, 8, 8, 10, 10, 8, 8, 103, 103] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 447 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113450 none CC1=NN(CC(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 10, 10, 20, 20, 20, 35, 35, 35, 103, 103, 103, 173, 201, 201, 201, 201, 201, 103, 103, 35, 1, 1, 2, 2, 2, 6, 6, 10, 10, 10, 10, 20, 35, 35, 35, 35, 103, 173, 173, 201, 201, 35, 35, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 49, 50, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 748 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113450 none CC1=NN(CC(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 200, 149, 94, 149, 94, 94, 50, 50, 50, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 50, 201, 201, 201, 201, 201, 200, 200, 149, 149, 149, 149, 94, 50, 50, 50, 50, 13, 6, 6, 4, 4, 50, 50, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 848 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113450 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113450/1 /scratch/stefan/7770410/working/building/REAL300020113450 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 503) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/503 `/scratch/stefan/7770410/working/3D/503' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1) `REAL300020113450.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113450 none CC1=NN(CC(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 23, 12, 6, 12, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 32, 44, 49, 49, 49, 49, 8, 8, 1, 36, 36, 36, 36, 36, 23, 23, 12, 12, 12, 12, 6, 1, 1, 1, 1, 8, 32, 32, 44, 44, 1, 1, 36, 36] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50]) total number of confs: 302 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113450 none CC1=NN(CC(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 81, 45, 22, 45, 22, 22, 8, 8, 8, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 8, 104, 104, 104, 104, 104, 81, 81, 45, 45, 45, 45, 22, 8, 8, 8, 8, 1, 8, 8, 10, 10, 8, 8, 104, 104] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 449 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113450 none CC1=NN(CC(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 10, 10, 20, 20, 20, 36, 36, 36, 104, 104, 104, 173, 201, 201, 201, 201, 201, 104, 104, 36, 1, 1, 2, 2, 2, 6, 6, 10, 10, 10, 10, 20, 36, 36, 36, 36, 104, 173, 173, 201, 201, 36, 36, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 49, 50, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 744 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113450 none CC1=NN(CC(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 200, 149, 94, 149, 94, 94, 49, 49, 49, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 49, 201, 201, 201, 201, 201, 200, 200, 149, 149, 149, 149, 94, 49, 49, 49, 49, 12, 6, 6, 4, 4, 49, 49, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 846 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113450 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113450 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113450/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113450/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113450 Building REAL300020113451 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113451' /scratch/stefan/7770410/working/building/REAL300020113451 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113451 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113451/0 /scratch/stefan/7770410/working/building/REAL300020113451 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/504 `/scratch/stefan/7770410/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN2N=NN=C12) `REAL300020113451.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113451 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN2N=NN=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 1, 1, 6, 18, 34, 34, 34, 34, 34, 34, 34, 34, 18, 6, 6, 6, 6, 1, 8, 8, 10, 10, 6, 6, 34, 34, 34] 51 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 106 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113451 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN2N=NN=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 27, 27, 27, 13, 13, 13, 5, 2, 1, 1, 1, 1, 1, 1, 13, 13, 27, 37, 51, 51, 51, 51, 51, 51, 51, 51, 37, 27, 27, 27, 27, 13, 5, 5, 2, 2, 27, 27, 51, 51, 51] 51 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 131 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113451 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN2N=NN=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 19, 24, 24, 24, 24, 24, 6, 6, 1, 6, 26, 26, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 6, 19, 19, 24, 24, 1, 1, 26, 26, 26] 51 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113451 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN2N=NN=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 26, 26, 26, 34, 34, 34, 49, 51, 51, 51, 51, 51, 34, 34, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 26, 26, 26, 26, 34, 49, 49, 51, 51, 26, 26, 1, 1, 1] 51 rigid atoms, others: [1, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 176 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113451 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113451/1 /scratch/stefan/7770410/working/building/REAL300020113451 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 505) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/505 `/scratch/stefan/7770410/working/3D/505' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN2N=NN=C12) `REAL300020113451.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113451/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113451 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN2N=NN=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 1, 1, 6, 18, 34, 34, 34, 34, 34, 34, 34, 34, 18, 6, 6, 6, 6, 1, 8, 8, 10, 10, 6, 6, 34, 34, 34] 51 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 106 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113451 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN2N=NN=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 27, 27, 27, 13, 13, 13, 5, 2, 1, 1, 1, 1, 1, 1, 13, 13, 27, 37, 51, 51, 51, 51, 51, 51, 51, 51, 37, 27, 27, 27, 27, 13, 5, 5, 2, 2, 27, 27, 51, 51, 51] 51 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 131 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113451 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN2N=NN=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 19, 24, 24, 24, 24, 24, 6, 6, 1, 6, 26, 26, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 6, 19, 19, 24, 24, 1, 1, 26, 26, 26] 51 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113451 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN2N=NN=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 26, 26, 26, 34, 34, 34, 49, 51, 51, 51, 51, 51, 34, 34, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 26, 26, 26, 26, 34, 49, 49, 51, 51, 26, 26, 1, 1, 1] 51 rigid atoms, others: [1, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 176 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113451 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113451 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113451/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113451/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113451 Building REAL300020113452 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113452' /scratch/stefan/7770410/working/building/REAL300020113452 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113452 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113452/0 /scratch/stefan/7770410/working/building/REAL300020113452 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/506 `/scratch/stefan/7770410/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(Cl)C(C)(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113452.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113452 none C=C(Cl)C(C)(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 16, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 68, 100, 36, 68, 68, 36, 36, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 12, 12, 12, 12, 1, 1, 9, 100, 100, 68, 68, 68, 68, 68, 68, 36, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 431 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113452 none C=C(Cl)C(C)(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 16, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 141, 201, 81, 141, 141, 81, 81, 56, 56, 56, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 56, 201, 201, 141, 141, 141, 141, 141, 141, 81, 56, 56, 56, 56, 15, 6, 6, 4, 4, 56, 56] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 772 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113452 none C=C(Cl)C(C)(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 16, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 13, 23, 6, 13, 13, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 31, 46, 59, 59, 59, 59, 9, 9, 1, 23, 23, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 9, 31, 31, 46, 46, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113452 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113452/1 /scratch/stefan/7770410/working/building/REAL300020113452 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 507) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/507 `/scratch/stefan/7770410/working/3D/507' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(Cl)C(C)(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113452.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113452 none C=C(Cl)C(C)(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 16, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 68, 102, 36, 68, 68, 36, 36, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 102, 102, 68, 68, 68, 68, 68, 68, 36, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 434 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113452 none C=C(Cl)C(C)(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 16, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 141, 201, 81, 141, 141, 81, 81, 56, 56, 56, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 56, 201, 201, 141, 141, 141, 141, 141, 141, 81, 56, 56, 56, 56, 15, 6, 6, 4, 4, 56, 56] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 772 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113452 none C=C(Cl)C(C)(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 16, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 13, 23, 6, 13, 13, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 30, 45, 57, 57, 57, 57, 9, 9, 1, 23, 23, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 9, 30, 30, 45, 45, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 295 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113452 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113452 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113452/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113452/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113452 Building REAL300020113453 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113453' /scratch/stefan/7770410/working/building/REAL300020113453 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113453 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113453/0 /scratch/stefan/7770410/working/building/REAL300020113453 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/508 `/scratch/stefan/7770410/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113453.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113453 none CC(C)N1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [35, 21, 35, 21, 21, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 22, 30, 37, 37, 37, 37, 5, 5, 1, 35, 35, 35, 35, 35, 35, 35, 21, 21, 6, 1, 1, 1, 1, 5, 22, 22, 30, 30, 1, 1] 91 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 240 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113453 none CC(C)N1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [55, 42, 55, 42, 42, 42, 42, 19, 19, 19, 5, 5, 5, 1, 1, 1, 1, 1, 8, 12, 15, 15, 15, 15, 1, 1, 5, 55, 55, 55, 55, 55, 55, 55, 42, 42, 19, 5, 5, 5, 5, 1, 8, 8, 12, 12, 5, 5] 91 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 213 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113453 none CC(C)N1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 21, 21, 21, 42, 42, 42, 74, 85, 90, 90, 90, 90, 42, 42, 21, 6, 6, 6, 6, 6, 6, 6, 1, 1, 8, 21, 21, 21, 21, 42, 74, 74, 85, 85, 21, 21] 91 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 35] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 318 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113453 none CC(C)N1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [89, 88, 89, 88, 88, 88, 88, 63, 63, 63, 36, 36, 36, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 36, 89, 89, 89, 89, 89, 89, 89, 88, 88, 63, 36, 36, 36, 36, 14, 6, 6, 4, 4, 36, 36] 89 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 239 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113453 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113453/1 /scratch/stefan/7770410/working/building/REAL300020113453 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 509) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/509 `/scratch/stefan/7770410/working/3D/509' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113453.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113453/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113453 none CC(C)N1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [35, 21, 35, 21, 21, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 22, 31, 38, 38, 38, 38, 5, 5, 1, 35, 35, 35, 35, 35, 35, 35, 21, 21, 6, 1, 1, 1, 1, 5, 22, 22, 31, 31, 1, 1] 92 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 246 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113453 none CC(C)N1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [55, 42, 55, 42, 42, 42, 42, 19, 19, 19, 5, 5, 5, 1, 1, 1, 1, 1, 8, 12, 15, 15, 15, 15, 1, 1, 5, 55, 55, 55, 55, 55, 55, 55, 42, 42, 19, 5, 5, 5, 5, 1, 8, 8, 12, 12, 5, 5] 92 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 213 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113453 none CC(C)N1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 21, 21, 21, 42, 42, 42, 75, 86, 91, 91, 91, 91, 42, 42, 21, 6, 6, 6, 6, 6, 6, 6, 1, 1, 8, 21, 21, 21, 21, 42, 75, 75, 86, 86, 21, 21] 92 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 35] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 321 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113453 none CC(C)N1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [90, 89, 90, 89, 89, 89, 89, 64, 64, 64, 37, 37, 37, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 37, 90, 90, 90, 90, 90, 90, 90, 89, 89, 64, 37, 37, 37, 37, 15, 6, 6, 4, 4, 37, 37] 90 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 240 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113453 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113453 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113453/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113453/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113453 Building REAL300020113454 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113454' /scratch/stefan/7770410/working/building/REAL300020113454 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113454 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113454/0 /scratch/stefan/7770410/working/building/REAL300020113454 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/510 `/scratch/stefan/7770410/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN(C(F)F)C=C1) `REAL300020113454.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113454 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN(C(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 13, 13, 13, 1, 1, 1, 1, 1, 7, 9, 9, 9, 9, 9, 1, 1, 13, 61, 128, 128, 128, 160, 160, 128, 128, 61, 13, 13, 13, 13, 1, 7, 7, 9, 9, 13, 13, 160, 128, 128] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 481 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113454 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN(C(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [122, 122, 42, 42, 42, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 42, 122, 201, 201, 201, 201, 201, 201, 201, 122, 42, 42, 42, 42, 7, 4, 4, 2, 2, 42, 42, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 466 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113454 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN(C(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 35, 50, 50, 50, 50, 50, 13, 13, 1, 6, 20, 20, 20, 53, 53, 20, 20, 6, 1, 1, 1, 1, 13, 35, 35, 50, 50, 1, 1, 53, 20, 20] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113454 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN(C(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 20, 20, 20, 128, 128, 128, 181, 201, 201, 201, 201, 201, 128, 128, 20, 1, 1, 1, 1, 10, 10, 1, 1, 7, 20, 20, 20, 20, 128, 181, 181, 201, 201, 20, 20, 10, 1, 1] 201 rigid atoms, others: [1, 40, 41, 19, 20, 21, 22, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 611 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113454 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113454/1 /scratch/stefan/7770410/working/building/REAL300020113454 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 511) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/511 `/scratch/stefan/7770410/working/3D/511' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN(C(F)F)C=C1) `REAL300020113454.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113454 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN(C(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 1, 1, 13, 61, 128, 128, 128, 159, 159, 128, 128, 61, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13, 159, 128, 128] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 478 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113454 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN(C(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [122, 122, 42, 42, 42, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 42, 122, 201, 201, 201, 201, 201, 201, 201, 122, 42, 42, 42, 42, 7, 4, 4, 2, 2, 42, 42, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 466 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113454 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN(C(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 35, 50, 50, 50, 50, 50, 13, 13, 1, 6, 20, 20, 20, 53, 53, 20, 20, 6, 1, 1, 1, 1, 13, 35, 35, 50, 50, 1, 1, 53, 20, 20] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113454 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN(C(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 20, 20, 20, 128, 128, 128, 181, 201, 201, 201, 201, 201, 128, 128, 20, 1, 1, 1, 1, 10, 10, 1, 1, 7, 20, 20, 20, 20, 128, 181, 181, 201, 201, 20, 20, 10, 1, 1] 201 rigid atoms, others: [1, 40, 41, 19, 20, 21, 22, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 611 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113454 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113454 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113454/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113454/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113454 Building REAL300020113455 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113455' /scratch/stefan/7770410/working/building/REAL300020113455 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113455 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113455/0 /scratch/stefan/7770410/working/building/REAL300020113455 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/512 `/scratch/stefan/7770410/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1C(F)F) `REAL300020113455.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113455 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1C(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 37, 83, 83, 83, 83, 83, 110, 110, 37, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 83, 83, 110] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 344 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113455 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1C(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 55, 55, 55, 13, 13, 13, 7, 4, 1, 1, 1, 1, 1, 1, 13, 13, 55, 118, 201, 201, 201, 201, 201, 201, 201, 118, 55, 55, 55, 55, 13, 7, 7, 4, 4, 55, 55, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 485 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113455 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1C(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 34, 47, 56, 56, 56, 56, 11, 11, 1, 6, 15, 15, 15, 15, 15, 32, 32, 6, 1, 1, 1, 1, 11, 34, 34, 47, 47, 1, 1, 15, 15, 32] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 308 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113455 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1C(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 15, 15, 15, 83, 83, 83, 150, 190, 201, 201, 201, 201, 83, 83, 15, 1, 1, 1, 1, 1, 1, 7, 7, 4, 15, 15, 15, 15, 83, 150, 150, 190, 190, 15, 15, 1, 1, 7] 201 rigid atoms, others: [1, 39, 40, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41]) total number of confs: 730 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113455 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113455/1 /scratch/stefan/7770410/working/building/REAL300020113455 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 513) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/513 `/scratch/stefan/7770410/working/3D/513' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1C(F)F) `REAL300020113455.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113455 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1C(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 36, 82, 82, 82, 82, 82, 111, 111, 36, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 82, 82, 111] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 354 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113455 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1C(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 54, 54, 54, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 54, 119, 201, 201, 201, 201, 201, 201, 201, 119, 54, 54, 54, 54, 12, 6, 6, 4, 4, 54, 54, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 482 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113455 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1C(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 35, 48, 57, 57, 57, 57, 11, 11, 1, 6, 15, 15, 15, 15, 15, 32, 32, 6, 1, 1, 1, 1, 11, 35, 35, 48, 48, 1, 1, 15, 15, 32] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 311 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113455 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1C(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 15, 15, 15, 82, 82, 82, 150, 191, 201, 201, 201, 201, 82, 82, 15, 1, 1, 1, 1, 1, 1, 7, 7, 4, 15, 15, 15, 15, 82, 150, 150, 191, 191, 15, 15, 1, 1, 7] 201 rigid atoms, others: [1, 39, 40, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41]) total number of confs: 739 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113455 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113455 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113455/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113455/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113455 Building REAL300020113456 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113456' /scratch/stefan/7770410/working/building/REAL300020113456 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113456 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113456/0 /scratch/stefan/7770410/working/building/REAL300020113456 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/514 `/scratch/stefan/7770410/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113456.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113456 none C=CC(C)(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 80, 50, 80, 80, 32, 32, 32, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 99, 99, 99, 80, 80, 80, 80, 80, 80, 50, 50, 32, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 459 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113456 none C=CC(C)(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 129, 201, 201, 78, 78, 78, 38, 38, 38, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 38, 201, 201, 201, 201, 201, 201, 201, 201, 201, 129, 129, 78, 38, 38, 38, 38, 7, 4, 4, 2, 2, 38, 38] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 937 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113456 none C=CC(C)(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 19, 11, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 29, 42, 43, 43, 43, 43, 11, 11, 1, 27, 27, 27, 19, 19, 19, 19, 19, 19, 11, 11, 6, 1, 1, 1, 1, 11, 29, 29, 42, 42, 1, 1] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 46, 47, 40, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113456 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113456/1 /scratch/stefan/7770410/working/building/REAL300020113456 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 515) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/515 `/scratch/stefan/7770410/working/3D/515' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113456.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113456 none C=CC(C)(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 80, 50, 80, 80, 32, 32, 32, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 99, 99, 99, 80, 80, 80, 80, 80, 80, 50, 50, 32, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 459 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113456 none C=CC(C)(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 129, 201, 201, 76, 76, 76, 38, 38, 38, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 38, 201, 201, 201, 201, 201, 201, 201, 201, 201, 129, 129, 76, 38, 38, 38, 38, 7, 4, 4, 2, 2, 38, 38] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 940 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113456 none C=CC(C)(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 19, 11, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 29, 42, 43, 43, 43, 43, 11, 11, 1, 27, 27, 27, 19, 19, 19, 19, 19, 19, 11, 11, 6, 1, 1, 1, 1, 11, 29, 29, 42, 42, 1, 1] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 46, 47, 40, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113456 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113456 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113456/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113456/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113456 Building REAL300020113457 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113457' /scratch/stefan/7770410/working/building/REAL300020113457 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113457 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113457/0 /scratch/stefan/7770410/working/building/REAL300020113457 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/516 `/scratch/stefan/7770410/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C(F)(F)F)OC=C1) `REAL300020113457.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113457 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C(F)(F)F)OC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 15, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 8, 11, 13, 13, 13, 13, 1, 1, 6, 20, 37, 37, 37, 37, 37, 37, 37, 37, 20, 6, 6, 6, 6, 1, 8, 8, 11, 11, 6, 6, 37, 37] 63 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 124 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113457 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C(F)(F)F)OC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 15, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 32, 32, 32, 17, 17, 17, 8, 4, 1, 1, 1, 1, 1, 1, 17, 17, 32, 48, 63, 63, 63, 63, 63, 63, 63, 63, 48, 32, 32, 32, 32, 17, 8, 8, 4, 4, 32, 32, 63, 63] 63 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 170 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113457 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C(F)(F)F)OC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 15, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 18, 27, 29, 29, 29, 29, 6, 6, 1, 6, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 6, 18, 18, 27, 27, 1, 1, 20, 20] 63 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113457 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C(F)(F)F)OC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 15, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 20, 20, 20, 37, 37, 37, 55, 63, 63, 63, 63, 63, 37, 37, 20, 1, 1, 1, 2, 2, 2, 1, 1, 1, 9, 20, 20, 20, 20, 37, 55, 55, 63, 63, 20, 20, 1, 1] 63 rigid atoms, others: [1, 40, 41, 19, 20, 21, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 229 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113457 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113457/1 /scratch/stefan/7770410/working/building/REAL300020113457 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 517) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/517 `/scratch/stefan/7770410/working/3D/517' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C(F)(F)F)OC=C1) `REAL300020113457.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113457/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113457 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C(F)(F)F)OC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 15, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 8, 11, 13, 13, 13, 13, 1, 1, 6, 20, 37, 37, 37, 37, 37, 37, 37, 37, 20, 6, 6, 6, 6, 1, 8, 8, 11, 11, 6, 6, 37, 37] 63 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 124 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113457 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C(F)(F)F)OC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 15, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 32, 32, 32, 17, 17, 17, 8, 4, 1, 1, 1, 1, 1, 1, 17, 17, 32, 48, 63, 63, 63, 63, 63, 63, 63, 63, 48, 32, 32, 32, 32, 17, 8, 8, 4, 4, 32, 32, 63, 63] 63 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 170 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113457 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C(F)(F)F)OC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 15, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 18, 27, 29, 29, 29, 29, 6, 6, 1, 6, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 6, 18, 18, 27, 27, 1, 1, 20, 20] 63 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113457 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C(F)(F)F)OC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 15, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 20, 20, 20, 37, 37, 37, 55, 63, 63, 63, 63, 63, 37, 37, 20, 1, 1, 1, 2, 2, 2, 1, 1, 1, 9, 20, 20, 20, 20, 37, 55, 55, 63, 63, 20, 20, 1, 1] 63 rigid atoms, others: [1, 40, 41, 19, 20, 21, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 229 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113457 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113457 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113457/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113457/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113457 Building REAL300020113458 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113458' /scratch/stefan/7770410/working/building/REAL300020113458 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113458 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113458/0 /scratch/stefan/7770410/working/building/REAL300020113458 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/518 `/scratch/stefan/7770410/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC(C)=N1) `REAL300020113458.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113458 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 50, 68, 82, 82, 82, 82, 12, 12, 1, 11, 11, 11, 6, 11, 11, 11, 11, 6, 1, 1, 1, 1, 12, 50, 50, 68, 68, 1, 1, 11, 11, 11, 11] 201 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46]) total number of confs: 330 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113458 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 40, 40, 40, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 12, 75, 75, 75, 40, 75, 75, 75, 75, 40, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 75, 75, 75, 75] 201 rigid atoms, others: [36, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 323 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113458 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 82, 82, 82, 155, 201, 201, 201, 201, 201, 82, 82, 11, 1, 1, 1, 1, 2, 2, 2, 1, 3, 11, 11, 11, 11, 82, 155, 155, 201, 201, 11, 11, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 43, 23, 24, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46]) total number of confs: 771 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113458 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 129, 129, 129, 87, 87, 87, 17, 17, 17, 7, 4, 1, 1, 1, 1, 1, 1, 17, 17, 87, 201, 201, 201, 132, 201, 201, 201, 201, 129, 87, 87, 87, 87, 17, 7, 7, 4, 4, 87, 87, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 715 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113458 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113458/1 /scratch/stefan/7770410/working/building/REAL300020113458 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 519) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/519 `/scratch/stefan/7770410/working/3D/519' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC(C)=N1) `REAL300020113458.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113458/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113458 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 50, 68, 81, 81, 81, 81, 12, 12, 1, 11, 11, 11, 6, 11, 11, 11, 11, 6, 1, 1, 1, 1, 12, 50, 50, 68, 68, 1, 1, 11, 11, 11, 11] 201 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46]) total number of confs: 328 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113458 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 40, 40, 40, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 12, 74, 74, 74, 40, 74, 74, 74, 74, 40, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 74, 74, 74, 74] 201 rigid atoms, others: [36, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 318 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113458 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 83, 83, 83, 156, 201, 201, 201, 201, 201, 83, 83, 12, 1, 1, 1, 1, 2, 2, 2, 1, 4, 12, 12, 12, 12, 83, 156, 156, 201, 201, 12, 12, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 43, 23, 24, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46]) total number of confs: 767 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113458 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 128, 128, 128, 86, 86, 86, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 86, 201, 201, 201, 129, 201, 201, 201, 201, 128, 86, 86, 86, 86, 15, 6, 6, 4, 4, 86, 86, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 723 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113458 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113458 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113458/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113458/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113458 Building REAL300020113459 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113459' /scratch/stefan/7770410/working/building/REAL300020113459 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113459 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113459/0 /scratch/stefan/7770410/working/building/REAL300020113459 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/520 `/scratch/stefan/7770410/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1CCC1) `REAL300020113459.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113459 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 50, 129, 129, 129, 129, 129, 140, 140, 140, 50, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 129, 129, 140, 140, 140, 140, 140, 140, 140] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 433 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113459 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 4, 19, 19, 43, 43, 43, 140, 140, 140, 186, 201, 201, 201, 201, 201, 140, 140, 43, 4, 4, 4, 1, 4, 1, 1, 1, 1, 19, 43, 43, 43, 43, 140, 186, 186, 201, 201, 43, 43, 4, 4, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 22, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 570 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113459 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 43, 43, 43, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 43, 109, 201, 201, 201, 201, 201, 201, 201, 201, 109, 43, 43, 43, 43, 9, 4, 4, 2, 2, 43, 43, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 601 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113459 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 30, 40, 40, 40, 40, 40, 13, 13, 1, 6, 30, 30, 30, 30, 30, 43, 43, 43, 6, 1, 1, 1, 1, 13, 30, 30, 40, 40, 1, 1, 30, 30, 43, 43, 43, 43, 43, 43, 43] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113459 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 30, 30, 30, 129, 129, 129, 179, 196, 196, 196, 196, 196, 129, 129, 30, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 30, 30, 30, 30, 129, 179, 179, 196, 196, 30, 30, 1, 1, 4, 4, 4, 4, 4, 4, 4] 201 rigid atoms, others: [1, 40, 41, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 567 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113459 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113459/1 /scratch/stefan/7770410/working/building/REAL300020113459 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 521) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/521 `/scratch/stefan/7770410/working/3D/521' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1CCC1) `REAL300020113459.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113459 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 50, 128, 128, 128, 128, 128, 139, 139, 139, 50, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 128, 128, 139, 139, 139, 139, 139, 139, 139] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 431 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113459 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 4, 19, 19, 43, 43, 43, 139, 139, 139, 185, 201, 201, 201, 201, 201, 139, 139, 43, 4, 4, 4, 1, 4, 1, 1, 1, 1, 19, 43, 43, 43, 43, 139, 185, 185, 201, 201, 43, 43, 4, 4, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 22, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 575 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113459 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 43, 43, 43, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 43, 110, 201, 201, 201, 201, 201, 201, 201, 201, 110, 43, 43, 43, 43, 8, 4, 4, 2, 2, 43, 43, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 601 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113459 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 30, 40, 40, 40, 40, 40, 13, 13, 1, 6, 30, 30, 30, 30, 30, 43, 43, 43, 6, 1, 1, 1, 1, 13, 30, 30, 40, 40, 1, 1, 30, 30, 43, 43, 43, 43, 43, 43, 43] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113459 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 30, 30, 30, 128, 128, 128, 178, 196, 196, 196, 196, 196, 128, 128, 30, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 30, 30, 30, 30, 128, 178, 178, 196, 196, 30, 30, 1, 1, 4, 4, 4, 4, 4, 4, 4] 201 rigid atoms, others: [1, 40, 41, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 572 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113459 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113459 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113459/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113459/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113459 Building REAL300020113460 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113460' /scratch/stefan/7770410/working/building/REAL300020113460 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113460 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113460/0 /scratch/stefan/7770410/working/building/REAL300020113460 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/522 `/scratch/stefan/7770410/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1) `REAL300020113460.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113460 none C[NH+](C)CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 72, 75, 75, 58, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 18, 18, 18, 18, 18, 18, 11, 11, 1, 19, 19, 75, 75, 75, 75, 75, 75, 72, 72, 58, 58, 19, 6, 1, 1, 1, 1, 11, 18, 18, 18, 18, 1, 1, 19] 201 rigid atoms, others: [45, 43, 44, 42, 11, 12, 13, 14, 15, 51, 52, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50, 53]) total number of confs: 348 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113460 none C[NH+](C)CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [188, 188, 188, 188, 173, 93, 93, 93, 30, 30, 30, 11, 11, 11, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 11, 93, 93, 188, 188, 188, 188, 188, 188, 188, 188, 173, 173, 93, 30, 11, 11, 11, 11, 1, 3, 3, 3, 3, 11, 11, 93] 201 rigid atoms, others: [46, 15, 16, 17, 18, 14, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 655 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113460 none C[NH+](C)CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 12, 15, 15, 7, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 19, 93, 93, 93, 110, 110, 110, 110, 110, 110, 93, 93, 19, 1, 1, 15, 15, 15, 15, 15, 15, 12, 12, 7, 7, 1, 5, 19, 19, 19, 19, 93, 110, 110, 110, 110, 19, 19, 1] 201 rigid atoms, others: [5, 6, 7, 8, 9, 40, 53, 28, 29] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 303 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113460 none C[NH+](C)CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 194, 110, 110, 110, 39, 39, 39, 17, 17, 17, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 17, 110, 110, 201, 201, 201, 201, 201, 201, 201, 201, 194, 194, 110, 39, 17, 17, 17, 17, 3, 3, 3, 1, 1, 17, 17, 110] 201 rigid atoms, others: [50, 49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 51, 52, 53]) total number of confs: 694 number of broken/clashed sets: 200 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113460 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113460/1 /scratch/stefan/7770410/working/building/REAL300020113460 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 523) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/523 `/scratch/stefan/7770410/working/3D/523' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1) `REAL300020113460.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113460 none C[NH+](C)CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 72, 75, 75, 58, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 18, 18, 18, 18, 18, 18, 11, 11, 1, 19, 19, 75, 75, 75, 75, 75, 75, 72, 72, 58, 58, 19, 6, 1, 1, 1, 1, 11, 18, 18, 18, 18, 1, 1, 19] 201 rigid atoms, others: [45, 43, 44, 42, 11, 12, 13, 14, 15, 51, 52, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50, 53]) total number of confs: 348 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113460 none C[NH+](C)CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [188, 188, 188, 188, 173, 93, 93, 93, 30, 30, 30, 11, 11, 11, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 11, 93, 93, 188, 188, 188, 188, 188, 188, 188, 188, 173, 173, 93, 30, 11, 11, 11, 11, 1, 3, 3, 3, 3, 11, 11, 93] 201 rigid atoms, others: [46, 15, 16, 17, 18, 14, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 655 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113460 none C[NH+](C)CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 12, 15, 15, 7, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 19, 93, 93, 93, 110, 110, 110, 110, 110, 110, 93, 93, 19, 1, 1, 15, 15, 15, 15, 15, 15, 12, 12, 7, 7, 1, 5, 19, 19, 19, 19, 93, 110, 110, 110, 110, 19, 19, 1] 201 rigid atoms, others: [5, 6, 7, 8, 9, 40, 53, 28, 29] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 303 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113460 none C[NH+](C)CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 194, 110, 110, 110, 39, 39, 39, 17, 17, 17, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 17, 110, 110, 201, 201, 201, 201, 201, 201, 201, 201, 194, 194, 110, 39, 17, 17, 17, 17, 3, 3, 3, 1, 1, 17, 17, 110] 201 rigid atoms, others: [50, 49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 51, 52, 53]) total number of confs: 694 number of broken/clashed sets: 200 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113460 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113460 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113460/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113460/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113460 Building REAL300020113461 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113461' /scratch/stefan/7770410/working/building/REAL300020113461 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113461 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113461/0 /scratch/stefan/7770410/working/building/REAL300020113461 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/524 `/scratch/stefan/7770410/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020113461.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113461 none CC1=CC=CC([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 38, 38, 38, 107, 107, 107, 120, 128, 128, 128, 128, 128, 107, 107, 38, 3, 3, 3, 3, 1, 3, 3, 1, 1, 11, 38, 38, 38, 38, 107, 120, 120, 128, 128, 38, 38, 3] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 321 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113461 none CC1=CC=CC([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 126, 201, 201, 126, 126, 126, 126, 75, 126, 75, 75, 29, 29, 29, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 29, 201, 201, 201, 201, 126, 201, 201, 126, 126, 75, 29, 29, 29, 29, 7, 4, 4, 2, 2, 29, 29, 201] 201 rigid atoms, others: [21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 755 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113461 none CC1=CC=CC([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 38, 61, 61, 38, 38, 38, 38, 6, 38, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 19, 25, 25, 25, 25, 25, 12, 12, 1, 61, 61, 61, 61, 38, 61, 61, 38, 38, 6, 1, 1, 1, 1, 12, 19, 19, 25, 25, 1, 1, 61] 201 rigid atoms, others: [49, 40, 41, 42, 43, 13, 14, 15, 16, 17, 50, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 51]) total number of confs: 292 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113461 none CC1=CC=CC([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 21, 21, 21, 61, 61, 61, 167, 167, 167, 188, 201, 201, 201, 201, 201, 167, 167, 61, 1, 2, 2, 2, 1, 1, 1, 3, 3, 21, 61, 61, 61, 61, 167, 188, 188, 201, 201, 61, 61, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 35, 36, 30, 51] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 510 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113461 none CC1=CC=CC([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [167, 167, 107, 167, 167, 107, 107, 107, 107, 42, 107, 42, 42, 12, 12, 12, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 1, 1, 12, 167, 167, 167, 167, 107, 167, 167, 107, 107, 42, 12, 12, 12, 12, 1, 3, 3, 5, 5, 12, 12, 167] 201 rigid atoms, others: [44, 16, 17, 18, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 614 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113461 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113461/1 /scratch/stefan/7770410/working/building/REAL300020113461 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 525) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/525 `/scratch/stefan/7770410/working/3D/525' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020113461.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113461/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113461 none CC1=CC=CC([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 38, 38, 38, 108, 108, 108, 121, 129, 129, 129, 129, 129, 108, 108, 38, 3, 3, 3, 3, 1, 3, 3, 1, 1, 11, 38, 38, 38, 38, 108, 121, 121, 129, 129, 38, 38, 3] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 322 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113461 none CC1=CC=CC([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 127, 201, 201, 127, 127, 127, 127, 75, 127, 75, 75, 29, 29, 29, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 29, 201, 201, 201, 201, 127, 201, 201, 127, 127, 75, 29, 29, 29, 29, 7, 4, 4, 2, 2, 29, 29, 201] 201 rigid atoms, others: [21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 754 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113461 none CC1=CC=CC([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 38, 61, 61, 38, 38, 38, 38, 6, 38, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 19, 25, 25, 25, 25, 25, 12, 12, 1, 61, 61, 61, 61, 38, 61, 61, 38, 38, 6, 1, 1, 1, 1, 12, 19, 19, 25, 25, 1, 1, 61] 201 rigid atoms, others: [49, 40, 41, 42, 43, 13, 14, 15, 16, 17, 50, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 51]) total number of confs: 292 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113461 none CC1=CC=CC([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 21, 21, 21, 61, 61, 61, 168, 168, 168, 189, 201, 201, 201, 201, 201, 168, 168, 61, 1, 2, 2, 2, 1, 1, 1, 3, 3, 21, 61, 61, 61, 61, 168, 189, 189, 201, 201, 61, 61, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 35, 36, 30, 51] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 505 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113461 none CC1=CC=CC([C@@H]2C[C@H]2C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [168, 168, 108, 168, 168, 108, 108, 108, 108, 43, 108, 43, 43, 12, 12, 12, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 1, 1, 12, 168, 168, 168, 168, 108, 168, 168, 108, 108, 43, 12, 12, 12, 12, 1, 3, 3, 5, 5, 12, 12, 168] 201 rigid atoms, others: [44, 16, 17, 18, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 616 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113461 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113461 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113461/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113461/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113461 Building REAL300020113462 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113462' /scratch/stefan/7770410/working/building/REAL300020113462 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113462 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113462/0 /scratch/stefan/7770410/working/building/REAL300020113462 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/526 `/scratch/stefan/7770410/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1[C@@H]1C[C@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113462.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113462 none CC1=CC=CC=C1[C@@H]1C[C@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 35, 35, 35, 125, 125, 125, 145, 154, 154, 154, 154, 154, 125, 125, 35, 3, 3, 3, 3, 2, 3, 3, 1, 1, 11, 35, 35, 35, 35, 125, 145, 145, 154, 154, 35, 35] 201 rigid atoms, others: [11, 6, 38, 7, 8, 9, 10, 39, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 374 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113462 none CC1=CC=CC=C1[C@@H]1C[C@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 160, 160, 160, 160, 83, 160, 83, 83, 34, 34, 34, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 34, 201, 201, 201, 201, 201, 201, 201, 160, 160, 83, 34, 34, 34, 34, 7, 4, 4, 2, 2, 34, 34] 201 rigid atoms, others: [22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 546 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113462 none CC1=CC=CC=C1[C@@H]1C[C@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 60, 60, 60, 35, 35, 35, 35, 6, 35, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 25, 32, 32, 32, 32, 32, 13, 13, 1, 60, 60, 60, 60, 60, 60, 60, 35, 35, 6, 1, 1, 1, 1, 13, 25, 25, 32, 32, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 50, 14, 15, 16, 17, 18, 51, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 249 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113462 none CC1=CC=CC=C1[C@@H]1C[C@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 21, 21, 21, 60, 60, 60, 170, 170, 170, 191, 201, 201, 201, 201, 201, 170, 170, 60, 2, 2, 2, 1, 1, 1, 1, 3, 3, 21, 60, 60, 60, 60, 170, 191, 191, 201, 201, 60, 60] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 36, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 489 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113462 none CC1=CC=CC=C1[C@@H]1C[C@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [170, 170, 170, 170, 170, 170, 125, 125, 125, 125, 48, 125, 48, 48, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 13, 170, 170, 170, 170, 170, 170, 170, 125, 125, 48, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13] 201 rigid atoms, others: [45, 17, 18, 19, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 458 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113462 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113462/1 /scratch/stefan/7770410/working/building/REAL300020113462 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 527) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/527 `/scratch/stefan/7770410/working/3D/527' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1[C@@H]1C[C@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113462.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113462/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113462 none CC1=CC=CC=C1[C@@H]1C[C@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 35, 35, 35, 125, 125, 125, 145, 154, 154, 154, 154, 154, 125, 125, 35, 3, 3, 3, 3, 2, 3, 3, 1, 1, 11, 35, 35, 35, 35, 125, 145, 145, 154, 154, 35, 35] 201 rigid atoms, others: [11, 6, 38, 7, 8, 9, 10, 39, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 374 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113462 none CC1=CC=CC=C1[C@@H]1C[C@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 161, 161, 161, 161, 83, 161, 83, 83, 34, 34, 34, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 34, 201, 201, 201, 201, 201, 201, 201, 161, 161, 83, 34, 34, 34, 34, 7, 4, 4, 2, 2, 34, 34] 201 rigid atoms, others: [22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 546 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113462 none CC1=CC=CC=C1[C@@H]1C[C@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 60, 60, 60, 35, 35, 35, 35, 6, 35, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 25, 32, 32, 32, 32, 32, 13, 13, 1, 60, 60, 60, 60, 60, 60, 60, 35, 35, 6, 1, 1, 1, 1, 13, 25, 25, 32, 32, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 50, 14, 15, 16, 17, 18, 51, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 249 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113462 none CC1=CC=CC=C1[C@@H]1C[C@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 21, 21, 21, 60, 60, 60, 170, 170, 170, 191, 201, 201, 201, 201, 201, 170, 170, 60, 2, 2, 2, 1, 1, 1, 1, 3, 3, 21, 60, 60, 60, 60, 170, 191, 191, 201, 201, 60, 60] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 36, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 489 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113462 none CC1=CC=CC=C1[C@@H]1C[C@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [170, 170, 170, 170, 170, 170, 125, 125, 125, 125, 48, 125, 48, 48, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 13, 170, 170, 170, 170, 170, 170, 170, 125, 125, 48, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13] 201 rigid atoms, others: [45, 17, 18, 19, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 458 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113462 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113462 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113462/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113462/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113462 Building REAL300020113463 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113463' /scratch/stefan/7770410/working/building/REAL300020113463 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113463 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113463/0 /scratch/stefan/7770410/working/building/REAL300020113463 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/528 `/scratch/stefan/7770410/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1(=O)=O) `REAL300020113463.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113463 none CN1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 37, 55, 61, 61, 61, 61, 13, 13, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 13, 37, 37, 55, 55, 1, 1] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 45, 46, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 298 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113463 none CN1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [130, 130, 130, 130, 59, 59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 130, 130, 130, 130, 130, 130, 130, 130, 130, 130, 130, 59, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [40, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 417 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113463 none CN1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 26, 26, 26, 130, 130, 130, 180, 201, 201, 201, 201, 201, 130, 130, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 26, 26, 26, 26, 130, 180, 180, 201, 201, 26, 26] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 34, 24, 25, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 586 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113463 none CN1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 158, 158, 158, 61, 61, 61, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 61, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 158, 61, 61, 61, 61, 10, 6, 6, 4, 4, 61, 61] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 589 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113463 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113463/1 /scratch/stefan/7770410/working/building/REAL300020113463 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 529) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/529 `/scratch/stefan/7770410/working/3D/529' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1(=O)=O) `REAL300020113463.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113463/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113463 none CN1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 35, 53, 59, 59, 59, 59, 13, 13, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 13, 35, 35, 53, 53, 1, 1] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 45, 46, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 292 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113463 none CN1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [132, 132, 132, 132, 59, 59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 132, 132, 132, 132, 132, 132, 132, 132, 132, 132, 132, 59, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [40, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 421 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113463 none CN1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 26, 26, 26, 132, 132, 132, 181, 201, 201, 201, 201, 201, 132, 132, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 26, 26, 26, 26, 132, 181, 181, 201, 201, 26, 26] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 34, 24, 25, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 579 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113463 none CN1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 155, 155, 155, 59, 59, 59, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 59, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 155, 59, 59, 59, 59, 11, 6, 6, 4, 4, 59, 59] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 597 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113463 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113463 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113463/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113463/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113463 Building REAL300020113464 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113464' /scratch/stefan/7770410/working/building/REAL300020113464 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113464 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113464/0 /scratch/stefan/7770410/working/building/REAL300020113464 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/530 `/scratch/stefan/7770410/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)[C@@H]1OCC[C@@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113464.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113464 none C=C(C)[C@@H]1OCC[C@@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 6, 10, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 22, 29, 30, 30, 30, 30, 6, 6, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 1, 1, 1, 1, 6, 22, 22, 29, 29, 1, 1] 45 rigid atoms, others: [48, 39, 40, 41, 42, 12, 13, 14, 15, 16, 49, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 140 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113464 none C=C(C)[C@@H]1OCC[C@@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 16, 21, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 8, 11, 12, 12, 12, 12, 1, 1, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 16, 6, 6, 6, 6, 1, 8, 8, 11, 11, 6, 6] 45 rigid atoms, others: [43, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 101 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113464 none C=C(C)[C@@H]1OCC[C@@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 21, 21, 21, 37, 45, 45, 45, 45, 45, 21, 21, 10, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 10, 10, 10, 10, 21, 37, 37, 45, 45, 10, 10] 45 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 35, 36, 37] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113464 none C=C(C)[C@@H]1OCC[C@@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 45, 45, 45, 44, 45, 44, 44, 31, 31, 31, 14, 14, 14, 5, 3, 1, 1, 1, 1, 1, 1, 14, 14, 31, 45, 45, 45, 45, 45, 45, 45, 45, 45, 44, 31, 31, 31, 31, 14, 5, 5, 3, 3, 31, 31] 45 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 125 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113464 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113464/1 /scratch/stefan/7770410/working/building/REAL300020113464 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 531) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/531 `/scratch/stefan/7770410/working/3D/531' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)[C@@H]1OCC[C@@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113464.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113464/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113464 none C=C(C)[C@@H]1OCC[C@@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 6, 10, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 21, 28, 29, 29, 29, 29, 6, 6, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 1, 1, 1, 1, 6, 21, 21, 28, 28, 1, 1] 44 rigid atoms, others: [48, 39, 40, 41, 42, 12, 13, 14, 15, 16, 49, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 137 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113464 none C=C(C)[C@@H]1OCC[C@@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 16, 21, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 8, 10, 11, 11, 11, 11, 1, 1, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 16, 6, 6, 6, 6, 1, 8, 8, 10, 10, 6, 6] 44 rigid atoms, others: [43, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 95 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113464 none C=C(C)[C@@H]1OCC[C@@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 21, 21, 21, 36, 44, 44, 44, 44, 44, 21, 21, 10, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 10, 10, 10, 10, 21, 36, 36, 44, 44, 10, 10] 44 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 35, 36, 37] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113464 none C=C(C)[C@@H]1OCC[C@@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 44, 44, 44, 43, 44, 43, 43, 30, 30, 30, 13, 13, 13, 5, 3, 1, 1, 1, 1, 1, 1, 13, 13, 30, 44, 44, 44, 44, 44, 44, 44, 44, 44, 43, 30, 30, 30, 30, 13, 5, 5, 3, 3, 30, 30] 44 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 124 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113464 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113464 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113464/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113464/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113464 Building REAL300020113465 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113465' /scratch/stefan/7770410/working/building/REAL300020113465 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113465 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113465/0 /scratch/stefan/7770410/working/building/REAL300020113465 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/532 `/scratch/stefan/7770410/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C[C@@H]1C[C@H]1C1=CC=CC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113465.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113465 none O=C(C[C@@H]1C[C@H]1C1=CC=CC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 7, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 24, 24, 56, 56, 56, 151, 151, 151, 187, 201, 201, 201, 201, 201, 151, 151, 56, 7, 7, 3, 3, 1, 1, 1, 1, 1, 24, 56, 56, 56, 56, 151, 187, 187, 201, 201, 56, 56] 201 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 577 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113465 none O=C(C[C@@H]1C[C@H]1C1=CC=CC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 184, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 34, 34, 34, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 34, 184, 184, 201, 201, 201, 201, 201, 201, 201, 76, 34, 34, 34, 34, 7, 4, 4, 2, 2, 34, 34] 201 rigid atoms, others: [22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 734 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113465 none O=C(C[C@@H]1C[C@H]1C1=CC=CC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 30, 55, 55, 55, 55, 55, 56, 56, 55, 56, 56, 1, 1, 1, 1, 1, 9, 9, 9, 22, 32, 32, 32, 32, 32, 9, 9, 1, 30, 30, 55, 55, 56, 56, 55, 56, 56, 6, 1, 1, 1, 1, 9, 22, 22, 32, 32, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 50, 14, 15, 16, 17, 18, 51, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 319 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113465 none O=C(C[C@@H]1C[C@H]1C1=CC=CC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 23, 23, 55, 55, 55, 151, 151, 151, 187, 201, 201, 201, 201, 201, 151, 151, 55, 6, 6, 1, 1, 3, 3, 1, 3, 3, 23, 55, 55, 55, 55, 151, 187, 187, 201, 201, 55, 55] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 34] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 583 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113465 none O=C(C[C@@H]1C[C@H]1C1=CC=CC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 120, 151, 151, 151, 151, 151, 151, 151, 151, 151, 151, 9, 9, 9, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 9, 120, 120, 151, 151, 151, 151, 151, 151, 151, 29, 9, 9, 9, 9, 1, 5, 5, 7, 7, 9, 9] 201 rigid atoms, others: [45, 17, 18, 19, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 564 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113465 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113465/1 /scratch/stefan/7770410/working/building/REAL300020113465 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 533) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/533 `/scratch/stefan/7770410/working/3D/533' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C[C@@H]1C[C@H]1C1=CC=CC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113465.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113465 none O=C(C[C@@H]1C[C@H]1C1=CC=CC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 7, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 24, 24, 57, 57, 57, 152, 152, 152, 187, 201, 201, 201, 201, 201, 152, 152, 57, 7, 7, 3, 3, 1, 1, 1, 1, 1, 24, 57, 57, 57, 57, 152, 187, 187, 201, 201, 57, 57] 201 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 573 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113465 none O=C(C[C@@H]1C[C@H]1C1=CC=CC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 183, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 34, 34, 34, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 34, 183, 183, 201, 201, 201, 201, 201, 201, 201, 76, 34, 34, 34, 34, 7, 4, 4, 2, 2, 34, 34] 201 rigid atoms, others: [22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 732 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113465 none O=C(C[C@@H]1C[C@H]1C1=CC=CC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 30, 56, 56, 56, 56, 56, 57, 57, 56, 57, 57, 1, 1, 1, 1, 1, 9, 9, 9, 22, 32, 32, 32, 32, 32, 9, 9, 1, 30, 30, 56, 56, 57, 57, 56, 57, 57, 6, 1, 1, 1, 1, 9, 22, 22, 32, 32, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 50, 14, 15, 16, 17, 18, 51, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 323 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113465 none O=C(C[C@@H]1C[C@H]1C1=CC=CC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 23, 23, 56, 56, 56, 152, 152, 152, 187, 201, 201, 201, 201, 201, 152, 152, 56, 6, 6, 1, 1, 3, 3, 1, 3, 3, 23, 56, 56, 56, 56, 152, 187, 187, 201, 201, 56, 56] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 34] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 579 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113465 none O=C(C[C@@H]1C[C@H]1C1=CC=CC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 121, 152, 152, 152, 152, 152, 152, 152, 152, 152, 152, 9, 9, 9, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 9, 121, 121, 152, 152, 152, 152, 152, 152, 152, 29, 9, 9, 9, 9, 1, 5, 5, 7, 7, 9, 9] 201 rigid atoms, others: [45, 17, 18, 19, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 567 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113465 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113465 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113465/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113465/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113465 Building REAL300020113466 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113466' /scratch/stefan/7770410/working/building/REAL300020113466 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113466 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113466/0 /scratch/stefan/7770410/working/building/REAL300020113466 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/534 `/scratch/stefan/7770410/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN(C2CCC2)N=N1) `REAL300020113466.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113466 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN(C2CCC2)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 7, 7, 7, 1, 1, 1, 1, 1, 7, 9, 12, 12, 12, 12, 1, 1, 7, 19, 47, 47, 47, 139, 139, 139, 47, 47, 19, 7, 7, 7, 7, 1, 7, 7, 9, 9, 7, 7, 47, 139, 139, 139, 139, 139, 139, 139] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 380 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113466 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN(C2CCC2)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 10, 49, 49, 96, 96, 96, 139, 139, 139, 187, 201, 201, 201, 201, 201, 139, 139, 96, 10, 10, 1, 1, 1, 1, 1, 10, 10, 49, 96, 96, 96, 96, 139, 187, 187, 201, 201, 96, 96, 10, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 675 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113466 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN(C2CCC2)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 58, 58, 58, 20, 20, 20, 7, 4, 1, 1, 1, 1, 1, 1, 20, 20, 58, 84, 129, 129, 129, 201, 201, 201, 129, 129, 84, 58, 58, 58, 58, 20, 7, 7, 4, 4, 58, 58, 129, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 583 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113466 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN(C2CCC2)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 27, 35, 44, 44, 44, 44, 7, 7, 1, 6, 24, 24, 24, 96, 96, 96, 24, 24, 6, 1, 1, 1, 1, 7, 27, 27, 35, 35, 1, 1, 24, 96, 96, 96, 96, 96, 96, 96] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 365 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113466 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN(C2CCC2)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 24, 24, 24, 47, 47, 47, 94, 112, 123, 123, 123, 123, 47, 47, 24, 1, 1, 1, 1, 10, 10, 10, 1, 1, 8, 24, 24, 24, 24, 47, 94, 94, 112, 112, 24, 24, 1, 10, 10, 10, 10, 10, 10, 10] 201 rigid atoms, others: [1, 40, 19, 20, 21, 22, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 456 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113466 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113466/1 /scratch/stefan/7770410/working/building/REAL300020113466 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 535) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/535 `/scratch/stefan/7770410/working/3D/535' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN(C2CCC2)N=N1) `REAL300020113466.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113466/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113466 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN(C2CCC2)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 7, 7, 7, 1, 1, 1, 1, 1, 7, 9, 13, 13, 13, 13, 1, 1, 7, 19, 47, 47, 47, 139, 139, 139, 47, 47, 19, 7, 7, 7, 7, 1, 7, 7, 9, 9, 7, 7, 47, 139, 139, 139, 139, 139, 139, 139] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 384 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113466 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN(C2CCC2)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 10, 49, 49, 96, 96, 96, 139, 139, 139, 187, 201, 201, 201, 201, 201, 139, 139, 96, 10, 10, 1, 1, 1, 1, 1, 10, 10, 49, 96, 96, 96, 96, 139, 187, 187, 201, 201, 96, 96, 10, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 678 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113466 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN(C2CCC2)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 60, 60, 60, 20, 20, 20, 7, 4, 1, 1, 1, 1, 1, 1, 20, 20, 60, 85, 129, 129, 129, 201, 201, 201, 129, 129, 85, 60, 60, 60, 60, 20, 7, 7, 4, 4, 60, 60, 129, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 580 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113466 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN(C2CCC2)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 26, 34, 44, 44, 44, 44, 7, 7, 1, 6, 24, 24, 24, 96, 96, 96, 24, 24, 6, 1, 1, 1, 1, 7, 26, 26, 34, 34, 1, 1, 24, 96, 96, 96, 96, 96, 96, 96] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 363 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113466 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN(C2CCC2)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 24, 24, 24, 47, 47, 47, 92, 110, 122, 122, 122, 122, 47, 47, 24, 1, 1, 1, 1, 10, 10, 10, 1, 1, 8, 24, 24, 24, 24, 47, 92, 92, 110, 110, 24, 24, 1, 10, 10, 10, 10, 10, 10, 10] 201 rigid atoms, others: [1, 40, 19, 20, 21, 22, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 449 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113466 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113466 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113466/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113466/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113466 Building REAL300020113467 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113467' /scratch/stefan/7770410/working/building/REAL300020113467 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113467 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113467/0 /scratch/stefan/7770410/working/building/REAL300020113467 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/536 `/scratch/stefan/7770410/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CSC=C1C(F)F) `REAL300020113467.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113467 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CSC=C1C(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 9, 9, 9, 9, 1, 1, 11, 37, 81, 81, 81, 81, 81, 109, 109, 37, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 81, 81, 109] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 365 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113467 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CSC=C1C(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 45, 45, 45, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 45, 113, 201, 201, 201, 201, 201, 201, 201, 113, 45, 45, 45, 45, 9, 5, 5, 3, 3, 45, 45, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 461 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113467 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CSC=C1C(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 34, 49, 49, 49, 49, 49, 11, 11, 1, 6, 21, 21, 21, 21, 21, 33, 33, 6, 1, 1, 1, 1, 11, 34, 34, 49, 49, 1, 1, 21, 21, 33] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 293 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113467 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CSC=C1C(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 21, 21, 21, 81, 81, 81, 147, 201, 201, 201, 201, 201, 81, 81, 21, 1, 1, 1, 1, 1, 1, 6, 6, 10, 21, 21, 21, 21, 81, 147, 147, 201, 201, 21, 21, 1, 1, 6] 201 rigid atoms, others: [1, 39, 40, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41]) total number of confs: 792 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113467 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113467/1 /scratch/stefan/7770410/working/building/REAL300020113467 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 537) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/537 `/scratch/stefan/7770410/working/3D/537' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CSC=C1C(F)F) `REAL300020113467.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113467/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113467 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CSC=C1C(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 10, 10, 10, 10, 1, 1, 11, 37, 82, 82, 82, 82, 82, 110, 110, 37, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 82, 82, 110] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 368 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113467 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CSC=C1C(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 47, 47, 47, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 47, 113, 201, 201, 201, 201, 201, 201, 201, 113, 47, 47, 47, 47, 10, 5, 5, 3, 3, 47, 47, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 460 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113467 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CSC=C1C(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 34, 49, 50, 50, 50, 50, 11, 11, 1, 6, 22, 22, 22, 22, 22, 34, 34, 6, 1, 1, 1, 1, 11, 34, 34, 49, 49, 1, 1, 22, 22, 34] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 296 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113467 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CSC=C1C(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 22, 22, 22, 82, 82, 82, 147, 200, 201, 201, 201, 201, 82, 82, 22, 1, 1, 1, 1, 1, 1, 6, 6, 10, 22, 22, 22, 22, 82, 147, 147, 200, 200, 22, 22, 1, 1, 6] 201 rigid atoms, others: [1, 39, 40, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41]) total number of confs: 783 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113467 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113467 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113467/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113467/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113467 Building REAL300020113468 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113468' /scratch/stefan/7770410/working/building/REAL300020113468 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113468 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113468/0 /scratch/stefan/7770410/working/building/REAL300020113468 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/538 `/scratch/stefan/7770410/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCCO1) `REAL300020113468.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113468 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 49, 67, 49, 49, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 11, 67, 80, 80, 80, 80, 80, 67, 67, 67, 67, 67, 67, 49, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 80, 80, 80, 80, 80, 80, 80, 80, 80] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 321 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113468 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [175, 143, 175, 143, 143, 77, 77, 77, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 77, 175, 201, 201, 201, 201, 201, 175, 175, 175, 175, 175, 175, 143, 77, 77, 77, 77, 15, 6, 6, 4, 4, 77, 77, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 693 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113468 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 12, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 50, 67, 76, 76, 76, 76, 11, 11, 1, 12, 15, 15, 15, 15, 15, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 11, 50, 50, 67, 67, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 44, 45, 21, 38, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 336 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113468 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 5, 5, 5, 15, 15, 15, 80, 80, 80, 162, 201, 201, 201, 201, 201, 80, 80, 15, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 5, 15, 15, 15, 15, 80, 162, 162, 201, 201, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 54, 46, 47, 48, 49, 50, 51, 52, 53, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 770 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113468 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113468/1 /scratch/stefan/7770410/working/building/REAL300020113468 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 539) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/539 `/scratch/stefan/7770410/working/3D/539' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCCO1) `REAL300020113468.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113468 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 49, 67, 49, 49, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 11, 67, 80, 80, 80, 80, 80, 67, 67, 67, 67, 67, 67, 49, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 80, 80, 80, 80, 80, 80, 80, 80, 80] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 321 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113468 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [174, 142, 174, 142, 142, 77, 77, 77, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 77, 174, 201, 201, 201, 201, 201, 174, 174, 174, 174, 174, 174, 142, 77, 77, 77, 77, 15, 6, 6, 4, 4, 77, 77, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 693 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113468 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 12, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 50, 67, 76, 76, 76, 76, 11, 11, 1, 12, 15, 15, 15, 15, 15, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 11, 50, 50, 67, 67, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 44, 45, 21, 38, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 336 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113468 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 5, 5, 5, 15, 15, 15, 80, 80, 80, 162, 201, 201, 201, 201, 201, 80, 80, 15, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 5, 15, 15, 15, 15, 80, 162, 162, 201, 201, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 54, 46, 47, 48, 49, 50, 51, 52, 53, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 770 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113468 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113468 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113468/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113468/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113468 Building REAL300020113469 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113469' /scratch/stefan/7770410/working/building/REAL300020113469 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113469 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113469/0 /scratch/stefan/7770410/working/building/REAL300020113469 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/540 `/scratch/stefan/7770410/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1C1CCC1) `REAL300020113469.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113469 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 11, 35, 62, 62, 62, 62, 62, 103, 103, 103, 35, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 62, 62, 103, 103, 103, 103, 103, 103, 103] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 318 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113469 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 9, 9, 26, 26, 26, 103, 103, 103, 155, 201, 201, 201, 201, 201, 103, 103, 26, 5, 5, 5, 5, 1, 1, 1, 1, 1, 9, 26, 26, 26, 26, 103, 155, 155, 201, 201, 26, 26, 5, 5, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 711 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113469 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 43, 43, 43, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 43, 95, 136, 136, 136, 136, 136, 201, 201, 201, 95, 43, 43, 43, 43, 8, 4, 4, 2, 2, 43, 43, 136, 136, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 605 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113469 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 28, 43, 43, 43, 43, 43, 11, 11, 1, 6, 13, 13, 13, 13, 13, 26, 26, 26, 6, 1, 1, 1, 1, 11, 28, 28, 43, 43, 1, 1, 13, 13, 26, 26, 26, 26, 26, 26, 26] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113469 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 13, 13, 13, 62, 62, 62, 101, 136, 136, 136, 136, 136, 62, 62, 13, 1, 1, 1, 1, 1, 1, 5, 5, 5, 4, 13, 13, 13, 13, 62, 101, 101, 136, 136, 13, 13, 1, 1, 5, 5, 5, 5, 5, 5, 5] 201 rigid atoms, others: [1, 40, 41, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 519 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113469 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113469/1 /scratch/stefan/7770410/working/building/REAL300020113469 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 541) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/541 `/scratch/stefan/7770410/working/3D/541' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1C1CCC1) `REAL300020113469.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113469 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 11, 35, 62, 62, 62, 62, 62, 103, 103, 103, 35, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 62, 62, 103, 103, 103, 103, 103, 103, 103] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 318 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113469 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 9, 9, 26, 26, 26, 103, 103, 103, 155, 201, 201, 201, 201, 201, 103, 103, 26, 5, 5, 5, 5, 1, 1, 1, 1, 1, 9, 26, 26, 26, 26, 103, 155, 155, 201, 201, 26, 26, 5, 5, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 711 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113469 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 44, 44, 44, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 44, 96, 137, 137, 137, 137, 137, 201, 201, 201, 96, 44, 44, 44, 44, 8, 4, 4, 2, 2, 44, 44, 137, 137, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 603 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113469 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 28, 43, 43, 43, 43, 43, 11, 11, 1, 6, 13, 13, 13, 13, 13, 26, 26, 26, 6, 1, 1, 1, 1, 11, 28, 28, 43, 43, 1, 1, 13, 13, 26, 26, 26, 26, 26, 26, 26] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113469 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 13, 13, 13, 62, 62, 62, 101, 136, 136, 136, 136, 136, 62, 62, 13, 1, 1, 1, 1, 1, 1, 5, 5, 5, 4, 13, 13, 13, 13, 62, 101, 101, 136, 136, 13, 13, 1, 1, 5, 5, 5, 5, 5, 5, 5] 201 rigid atoms, others: [1, 40, 41, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 519 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113469 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113469 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113469/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113469/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113469 Building REAL300020113470 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113470' /scratch/stefan/7770410/working/building/REAL300020113470 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113470 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113470/0 /scratch/stefan/7770410/working/building/REAL300020113470 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/542 `/scratch/stefan/7770410/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CCN1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1) `REAL300020113470.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113470 none C[NH+](C)CCN1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 10, 10, 10, 10, 6, 6, 6, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 10, 10, 6, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1] 16 rigid atoms, others: [45, 44, 43, 12, 13, 14, 15, 16, 52, 46, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 57 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113470 none C[NH+](C)CCN1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 3, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 11, 11, 11, 3, 3, 3, 3, 1, 3, 3, 3, 3, 3, 3] 16 rigid atoms, others: [15, 47, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 66 number of broken/clashed sets: 15 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113470 none C[NH+](C)CCN1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 1, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 1, 1, 4, 10, 10, 10, 10, 11, 11, 11, 11, 11, 10, 10] 16 rigid atoms, others: [5, 6, 7, 8, 9, 10, 40, 41, 29] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 47 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113470 none C[NH+](C)CCN1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 11, 11, 11, 5, 5, 5, 5, 3, 3, 3, 1, 1, 5, 5] 15 rigid atoms, others: [19, 50, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 60 number of broken/clashed sets: 14 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113470 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113470/1 /scratch/stefan/7770410/working/building/REAL300020113470 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 543) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/543 `/scratch/stefan/7770410/working/3D/543' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CCN1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1) `REAL300020113470.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113470 none C[NH+](C)CCN1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 10, 10, 10, 10, 6, 6, 6, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 10, 10, 6, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1] 16 rigid atoms, others: [45, 44, 43, 12, 13, 14, 15, 16, 52, 46, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 57 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113470 none C[NH+](C)CCN1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 3, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 11, 11, 11, 3, 3, 3, 3, 1, 3, 3, 3, 3, 3, 3] 16 rigid atoms, others: [15, 47, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 66 number of broken/clashed sets: 15 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113470 none C[NH+](C)CCN1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 1, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 1, 1, 4, 10, 10, 10, 10, 11, 11, 11, 11, 11, 10, 10] 16 rigid atoms, others: [5, 6, 7, 8, 9, 10, 40, 41, 29] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 47 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113470 none C[NH+](C)CCN1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 11, 11, 11, 5, 5, 5, 5, 3, 3, 3, 1, 1, 5, 5] 15 rigid atoms, others: [19, 50, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 60 number of broken/clashed sets: 14 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113470 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113470 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113470/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113470/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113470 Building REAL300020113471 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113471' /scratch/stefan/7770410/working/building/REAL300020113471 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113471 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113471/0 /scratch/stefan/7770410/working/building/REAL300020113471 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/544 `/scratch/stefan/7770410/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1) `REAL300020113471.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113471 none CC(C)(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 10, 19, 19, 10, 10, 10, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 51, 71, 93, 93, 93, 93, 13, 13, 1, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 10, 6, 1, 1, 1, 1, 13, 51, 51, 71, 71, 1, 1, 10] 201 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 44, 50, 51, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 52]) total number of confs: 390 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113471 none CC(C)(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 70, 102, 102, 70, 70, 70, 53, 53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 15, 15, 15, 15, 1, 1, 13, 70, 70, 102, 102, 102, 102, 102, 102, 102, 102, 102, 70, 70, 53, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13, 70] 201 rigid atoms, others: [45, 14, 13, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 398 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113471 none CC(C)(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 70, 70, 70, 163, 190, 201, 201, 201, 201, 70, 70, 10, 1, 1, 4, 4, 4, 3, 3, 3, 4, 4, 4, 1, 1, 4, 10, 10, 10, 10, 70, 163, 163, 190, 190, 10, 10, 1] 201 rigid atoms, others: [1, 4, 38, 6, 7, 8, 39, 52, 27, 28, 5] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 724 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113471 none CC(C)(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 93, 93, 93, 16, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 93, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 93, 93, 93, 93, 16, 6, 6, 4, 4, 93, 93, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 570 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113471 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113471/1 /scratch/stefan/7770410/working/building/REAL300020113471 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 545) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/545 `/scratch/stefan/7770410/working/3D/545' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1) `REAL300020113471.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113471/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113471 none CC(C)(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 10, 19, 19, 10, 10, 10, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 51, 71, 92, 92, 92, 92, 13, 13, 1, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 10, 6, 1, 1, 1, 1, 13, 51, 51, 71, 71, 1, 1, 10] 201 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 44, 50, 51, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 52]) total number of confs: 388 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113471 none CC(C)(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 70, 103, 103, 70, 70, 70, 53, 53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 15, 15, 15, 15, 1, 1, 13, 70, 70, 103, 103, 103, 103, 103, 103, 103, 103, 103, 70, 70, 53, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13, 70] 201 rigid atoms, others: [45, 14, 13, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 404 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113471 none CC(C)(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 70, 70, 70, 163, 190, 201, 201, 201, 201, 70, 70, 10, 1, 1, 4, 4, 4, 3, 3, 3, 4, 4, 4, 1, 1, 4, 10, 10, 10, 10, 70, 163, 163, 190, 190, 10, 10, 1] 201 rigid atoms, others: [1, 4, 38, 6, 7, 8, 39, 52, 27, 28, 5] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 724 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113471 none CC(C)(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 93, 93, 93, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 93, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 93, 93, 93, 93, 15, 6, 6, 4, 4, 93, 93, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 571 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113471 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113471 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113471/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113471/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113471 Building REAL300020113472 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113472' /scratch/stefan/7770410/working/building/REAL300020113472 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113472 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113472/0 /scratch/stefan/7770410/working/building/REAL300020113472 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/546 `/scratch/stefan/7770410/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1C) `REAL300020113472.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113472 none CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [19, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 3, 19, 26, 26, 26, 26, 26, 19, 19, 19, 19, 7, 3, 3, 3, 3, 1, 5, 5, 5, 5, 3, 3, 26, 26, 26, 26, 26] 28 rigid atoms, others: [36, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 99 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113472 none CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [23, 11, 11, 11, 6, 6, 6, 6, 6, 6, 4, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 23, 28, 28, 28, 28, 28, 23, 23, 23, 23, 11, 6, 6, 6, 6, 6, 4, 4, 2, 2, 6, 6, 28, 28, 28, 28, 28] 28 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 97 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113472 none CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [19, 5, 5, 5, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 3, 3, 1, 19, 26, 26, 26, 26, 26, 19, 19, 19, 19, 5, 1, 1, 1, 1, 3, 5, 5, 5, 5, 1, 1, 26, 26, 26, 26, 26] 28 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 41, 42, 20] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47]) total number of confs: 94 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113472 none CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 20, 20, 20, 26, 26, 26, 26, 26, 26, 28, 28, 28, 28, 28, 28, 26, 26, 26, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 20, 26, 26, 26, 26, 26, 28, 28, 28, 28, 26, 26, 1, 1, 2, 2, 2] 28 rigid atoms, others: [1, 43, 44, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 97 number of broken/clashed sets: 3 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113472 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113472/1 /scratch/stefan/7770410/working/building/REAL300020113472 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 547) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/547 `/scratch/stefan/7770410/working/3D/547' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1C) `REAL300020113472.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113472/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113472 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [19, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 3, 19, 26, 26, 26, 26, 26, 19, 19, 19, 19, 7, 3, 3, 3, 3, 1, 5, 5, 5, 5, 3, 3, 26, 26, 26, 26, 26] 28 rigid atoms, others: [36, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 99 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113472 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [23, 11, 11, 11, 6, 6, 6, 6, 6, 6, 4, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 23, 28, 28, 28, 28, 28, 23, 23, 23, 23, 11, 6, 6, 6, 6, 6, 4, 4, 2, 2, 6, 6, 28, 28, 28, 28, 28] 28 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 97 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113472 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [19, 5, 5, 5, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 3, 3, 1, 19, 26, 26, 26, 26, 26, 19, 19, 19, 19, 5, 1, 1, 1, 1, 3, 5, 5, 5, 5, 1, 1, 26, 26, 26, 26, 26] 28 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 41, 42, 20] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47]) total number of confs: 94 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113472 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 20, 20, 20, 26, 26, 26, 26, 26, 26, 28, 28, 28, 28, 28, 28, 26, 26, 26, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 20, 26, 26, 26, 26, 26, 28, 28, 28, 28, 26, 26, 1, 1, 2, 2, 2] 28 rigid atoms, others: [1, 43, 44, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 97 number of broken/clashed sets: 3 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113472 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113472 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113472/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113472/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113472 Building REAL300020113473 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113473' /scratch/stefan/7770410/working/building/REAL300020113473 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113473 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113473/0 /scratch/stefan/7770410/working/building/REAL300020113473 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/548 `/scratch/stefan/7770410/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NSC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020113473.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113473 none COC1=NSC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 26, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 20, 28, 32, 32, 32, 32, 5, 5, 1, 26, 26, 26, 26, 6, 1, 1, 1, 1, 5, 20, 20, 28, 28, 1, 1, 26] 90 rigid atoms, others: [32, 33, 39, 8, 9, 10, 11, 12, 40, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41]) total number of confs: 156 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113473 none COC1=NSC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 51, 51, 18, 18, 18, 5, 5, 5, 1, 1, 1, 1, 1, 8, 11, 14, 14, 14, 14, 1, 1, 5, 51, 51, 51, 51, 18, 5, 5, 5, 5, 1, 8, 8, 11, 11, 5, 5, 51] 90 rigid atoms, others: [34, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 142 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113473 none COC1=NSC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 26, 26, 26, 51, 51, 51, 79, 90, 90, 90, 90, 90, 51, 51, 26, 1, 2, 2, 2, 8, 26, 26, 26, 26, 51, 79, 79, 90, 90, 26, 26, 1] 90 rigid atoms, others: [1, 2, 3, 4, 5, 6, 41, 25] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 307 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113473 none COC1=NSC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 91, 91, 56, 56, 56, 33, 33, 33, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 33, 91, 91, 91, 91, 56, 33, 33, 33, 33, 15, 6, 6, 4, 4, 33, 33, 91] 91 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 230 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113473 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113473/1 /scratch/stefan/7770410/working/building/REAL300020113473 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 549) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/549 `/scratch/stefan/7770410/working/3D/549' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NSC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020113473.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113473 none COC1=NSC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 26, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 20, 28, 32, 32, 32, 32, 5, 5, 1, 26, 26, 26, 26, 6, 1, 1, 1, 1, 5, 20, 20, 28, 28, 1, 1, 26] 90 rigid atoms, others: [32, 33, 39, 8, 9, 10, 11, 12, 40, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41]) total number of confs: 156 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113473 none COC1=NSC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 51, 51, 18, 18, 18, 5, 5, 5, 1, 1, 1, 1, 1, 8, 11, 14, 14, 14, 14, 1, 1, 5, 51, 51, 51, 51, 18, 5, 5, 5, 5, 1, 8, 8, 11, 11, 5, 5, 51] 90 rigid atoms, others: [34, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 142 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113473 none COC1=NSC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 26, 26, 26, 51, 51, 51, 79, 90, 90, 90, 90, 90, 51, 51, 26, 1, 2, 2, 2, 8, 26, 26, 26, 26, 51, 79, 79, 90, 90, 26, 26, 1] 90 rigid atoms, others: [1, 2, 3, 4, 5, 6, 41, 25] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 307 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113473 none COC1=NSC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 91, 91, 56, 56, 56, 33, 33, 33, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 33, 91, 91, 91, 91, 56, 33, 33, 33, 33, 15, 6, 6, 4, 4, 33, 33, 91] 91 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 230 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113473 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113473 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113473/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113473/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113473 Building REAL300020113474 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113474' /scratch/stefan/7770410/working/building/REAL300020113474 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113474 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113474/0 /scratch/stefan/7770410/working/building/REAL300020113474 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/550 `/scratch/stefan/7770410/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN2CCCC2=N1) `REAL300020113474.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113474 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN2CCCC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 19, 19, 19, 19, 1, 1, 13, 54, 88, 88, 88, 88, 88, 88, 88, 54, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 88, 88, 88, 88, 88, 88, 88] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 253 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113474 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN2CCCC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [191, 191, 115, 115, 115, 21, 21, 21, 6, 4, 1, 1, 1, 1, 1, 1, 21, 21, 115, 191, 201, 201, 201, 201, 201, 201, 201, 191, 115, 115, 115, 115, 21, 6, 6, 4, 4, 115, 115, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 545 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113474 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN2CCCC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 71, 95, 115, 115, 115, 115, 13, 13, 1, 6, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 13, 71, 71, 95, 95, 1, 1, 21, 21, 21, 21, 21, 21, 21] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 440 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113474 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN2CCCC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 21, 21, 21, 88, 88, 88, 169, 201, 201, 201, 201, 201, 88, 88, 21, 1, 1, 1, 1, 1, 1, 1, 1, 6, 21, 21, 21, 21, 88, 169, 169, 201, 201, 21, 21, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 39, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 685 number of broken/clashed sets: 2 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113474 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113474/1 /scratch/stefan/7770410/working/building/REAL300020113474 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 551) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/551 `/scratch/stefan/7770410/working/3D/551' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN2CCCC2=N1) `REAL300020113474.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113474 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN2CCCC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 19, 19, 19, 19, 1, 1, 13, 53, 86, 86, 86, 86, 86, 86, 86, 53, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 86, 86, 86, 86, 86, 86, 86] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 251 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113474 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN2CCCC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [192, 192, 116, 116, 116, 21, 21, 21, 6, 4, 1, 1, 1, 1, 1, 1, 21, 21, 116, 192, 201, 201, 201, 201, 201, 201, 201, 192, 116, 116, 116, 116, 21, 6, 6, 4, 4, 116, 116, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 547 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113474 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN2CCCC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 72, 96, 116, 116, 116, 116, 13, 13, 1, 6, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 13, 72, 72, 96, 96, 1, 1, 20, 20, 20, 20, 20, 20, 20] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 442 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113474 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN2CCCC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 20, 20, 20, 86, 86, 86, 167, 201, 201, 201, 201, 201, 86, 86, 20, 1, 1, 1, 1, 1, 1, 1, 1, 6, 20, 20, 20, 20, 86, 167, 167, 201, 201, 20, 20, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 39, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 697 number of broken/clashed sets: 2 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113474 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113474 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113474/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113474/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113474 Building REAL300020113475 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113475' /scratch/stefan/7770410/working/building/REAL300020113475 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113475 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113475/0 /scratch/stefan/7770410/working/building/REAL300020113475 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/552 `/scratch/stefan/7770410/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=NC=C1) `REAL300020113475.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113475 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 13, 52, 144, 144, 144, 144, 144, 144, 144, 144, 144, 144, 52, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 144, 144, 144, 144, 144, 144] 201 rigid atoms, others: [35, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 424 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113475 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 3, 16, 16, 37, 37, 37, 144, 144, 144, 177, 201, 201, 201, 201, 201, 144, 144, 37, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 16, 37, 37, 37, 37, 144, 177, 177, 201, 201, 37, 37, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 22, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 553 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113475 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 48, 48, 48, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 48, 114, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 114, 48, 48, 48, 48, 8, 4, 4, 2, 2, 48, 48, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 590 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113475 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 30, 45, 45, 45, 45, 45, 13, 13, 1, 6, 34, 34, 34, 34, 34, 37, 37, 34, 37, 37, 6, 1, 1, 1, 1, 13, 30, 30, 45, 45, 1, 1, 34, 34, 37, 37, 37, 37] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 40, 41, 34, 18, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113475 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 34, 34, 34, 144, 144, 144, 177, 201, 201, 201, 201, 201, 144, 144, 34, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 11, 34, 34, 34, 34, 144, 177, 177, 201, 201, 34, 34, 1, 1, 3, 3, 3, 3] 201 rigid atoms, others: [1, 42, 43, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 553 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113475 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113475/1 /scratch/stefan/7770410/working/building/REAL300020113475 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 553) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/553 `/scratch/stefan/7770410/working/3D/553' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=NC=C1) `REAL300020113475.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113475/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113475 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 13, 52, 144, 144, 144, 144, 144, 144, 144, 144, 144, 144, 52, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 144, 144, 144, 144, 144, 144] 201 rigid atoms, others: [35, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 424 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113475 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 3, 16, 16, 37, 37, 37, 144, 144, 144, 177, 201, 201, 201, 201, 201, 144, 144, 37, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 16, 37, 37, 37, 37, 144, 177, 177, 201, 201, 37, 37, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 22, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 553 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113475 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 48, 48, 48, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 48, 114, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 114, 48, 48, 48, 48, 8, 4, 4, 2, 2, 48, 48, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 590 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113475 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 30, 45, 45, 45, 45, 45, 13, 13, 1, 6, 34, 34, 34, 34, 34, 37, 37, 34, 37, 37, 6, 1, 1, 1, 1, 13, 30, 30, 45, 45, 1, 1, 34, 34, 37, 37, 37, 37] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 40, 41, 34, 18, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113475 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 34, 34, 34, 144, 144, 144, 177, 201, 201, 201, 201, 201, 144, 144, 34, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 11, 34, 34, 34, 34, 144, 177, 177, 201, 201, 34, 34, 1, 1, 3, 3, 3, 3] 201 rigid atoms, others: [1, 42, 43, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 553 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113475 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113475 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113475/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113475/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113475 Building REAL300020113476 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113476' /scratch/stefan/7770410/working/building/REAL300020113476 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for REAL300020113476 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113476/0 /scratch/stefan/7770410/working/building/REAL300020113476 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/554 `/scratch/stefan/7770410/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC[N@@H+]1C) `REAL300020113476.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113476 none C[C@@H]1[C@H](C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 6, 16, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 27, 27, 27, 27, 27, 27, 13, 13, 1, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 27, 27, 27, 27, 1, 1, 16, 16, 16, 16, 16, 16, 16] 57 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 131 number of broken/clashed sets: 57 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113476 none C[C@@H]1[C@H](C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 41, 48, 41, 41, 13, 13, 13, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 13, 48, 48, 48, 48, 48, 48, 48, 48, 41, 13, 13, 13, 13, 1, 5, 5, 5, 5, 13, 13, 48, 48, 48, 48, 48, 48, 48] 57 rigid atoms, others: [37, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 148 number of broken/clashed sets: 57 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113476 none C[C@@H]1[C@H](C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 48, 48, 48, 57, 57, 57, 57, 57, 57, 48, 48, 16, 1, 1, 1, 1, 1, 2, 2, 2, 6, 16, 16, 16, 16, 48, 57, 57, 57, 57, 16, 16, 1, 1, 1, 1, 2, 2, 2] 57 rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 45, 46, 47, 24, 25, 26, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113476 none C[C@@H]1[C@H](C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 53, 57, 53, 53, 27, 27, 27, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 27, 57, 57, 57, 57, 57, 57, 57, 57, 53, 27, 27, 27, 27, 5, 3, 3, 1, 1, 27, 27, 57, 57, 57, 57, 57, 57, 57] 57 rigid atoms, others: [40, 41, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 168 number of broken/clashed sets: 57 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113476 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113476/1 /scratch/stefan/7770410/working/building/REAL300020113476 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 555) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/555 `/scratch/stefan/7770410/working/3D/555' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC[N@H+]1C) `REAL300020113476.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113476/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113476 none C[C@@H]1[C@H](C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 6, 10, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 10, 10, 10, 10, 10, 10, 8, 8, 1, 10, 10, 10, 10, 10, 10, 10, 10, 6, 1, 1, 1, 1, 8, 10, 10, 10, 10, 1, 1, 10, 10, 10, 10, 10, 10, 10] 24 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 47 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113476 none C[C@@H]1[C@H](C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 21, 22, 21, 21, 8, 8, 8, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 8, 22, 22, 22, 22, 22, 22, 22, 22, 21, 8, 8, 8, 8, 1, 4, 4, 4, 4, 8, 8, 22, 22, 22, 22, 22, 22, 22] 24 rigid atoms, others: [37, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 71 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113476 none C[C@@H]1[C@H](C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 22, 22, 22, 24, 24, 24, 24, 24, 24, 22, 22, 10, 1, 1, 1, 1, 1, 2, 2, 2, 5, 10, 10, 10, 10, 22, 24, 24, 24, 24, 10, 10, 1, 1, 1, 1, 2, 2, 2] 24 rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 45, 46, 47, 24, 25, 26, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50]) total number of confs: 69 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113476 none C[C@@H]1[C@H](C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 23, 24, 23, 23, 10, 10, 10, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 24, 24, 24, 24, 24, 24, 24, 24, 23, 10, 10, 10, 10, 4, 3, 3, 1, 1, 10, 10, 24, 24, 24, 24, 24, 24, 24] 24 rigid atoms, others: [40, 41, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 70 number of broken/clashed sets: 10 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113476 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `2' /scratch/stefan/7770410/working/building/REAL300020113476/2 /scratch/stefan/7770410/working/building/REAL300020113476 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 2 (index: 556) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/556 `/scratch/stefan/7770410/working/3D/556' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC[N@@H+]1C) `REAL300020113476.mol2' -> `2.mol2' `temp.mol2' -> `REAL300020113476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113476/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113476 none C[C@@H]1[C@H](C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 6, 16, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 27, 27, 27, 27, 27, 27, 13, 13, 1, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 27, 27, 27, 27, 1, 1, 16, 16, 16, 16, 16, 16, 16] 57 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 131 number of broken/clashed sets: 57 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113476 none C[C@@H]1[C@H](C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 41, 48, 41, 41, 13, 13, 13, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 13, 48, 48, 48, 48, 48, 48, 48, 48, 41, 13, 13, 13, 13, 1, 5, 5, 5, 5, 13, 13, 48, 48, 48, 48, 48, 48, 48] 57 rigid atoms, others: [37, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 148 number of broken/clashed sets: 57 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113476 none C[C@@H]1[C@H](C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 48, 48, 48, 57, 57, 57, 57, 57, 57, 48, 48, 16, 1, 1, 1, 1, 1, 2, 2, 2, 6, 16, 16, 16, 16, 48, 57, 57, 57, 57, 16, 16, 1, 1, 1, 1, 2, 2, 2] 57 rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 45, 46, 47, 24, 25, 26, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113476 none C[C@@H]1[C@H](C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 53, 57, 53, 53, 27, 27, 27, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 27, 57, 57, 57, 57, 57, 57, 57, 57, 53, 27, 27, 27, 27, 5, 3, 3, 1, 1, 27, 27, 57, 57, 57, 57, 57, 57, 57] 57 rigid atoms, others: [40, 41, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 168 number of broken/clashed sets: 57 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113476 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `3' /scratch/stefan/7770410/working/building/REAL300020113476/3 /scratch/stefan/7770410/working/building/REAL300020113476 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 3 (index: 557) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/557 `/scratch/stefan/7770410/working/3D/557' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC[N@H+]1C) `REAL300020113476.mol2' -> `3.mol2' `temp.mol2' -> `REAL300020113476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113476/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113476 none C[C@@H]1[C@H](C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 6, 10, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 10, 10, 10, 10, 10, 10, 8, 8, 1, 10, 10, 10, 10, 10, 10, 10, 10, 6, 1, 1, 1, 1, 8, 10, 10, 10, 10, 1, 1, 10, 10, 10, 10, 10, 10, 10] 24 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 47 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113476 none C[C@@H]1[C@H](C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 21, 22, 21, 21, 8, 8, 8, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 8, 22, 22, 22, 22, 22, 22, 22, 22, 21, 8, 8, 8, 8, 1, 4, 4, 4, 4, 8, 8, 22, 22, 22, 22, 22, 22, 22] 24 rigid atoms, others: [37, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 71 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113476 none C[C@@H]1[C@H](C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 22, 22, 22, 24, 24, 24, 24, 24, 24, 22, 22, 10, 1, 1, 1, 1, 1, 2, 2, 2, 5, 10, 10, 10, 10, 22, 24, 24, 24, 24, 10, 10, 1, 1, 1, 1, 2, 2, 2] 24 rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 45, 46, 47, 24, 25, 26, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50]) total number of confs: 69 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113476 none C[C@@H]1[C@H](C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 23, 24, 23, 23, 10, 10, 10, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 24, 24, 24, 24, 24, 24, 24, 24, 23, 10, 10, 10, 10, 4, 3, 3, 1, 1, 10, 10, 24, 24, 24, 24, 24, 24, 24] 24 rigid atoms, others: [40, 41, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 70 number of broken/clashed sets: 10 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113476 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113476 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 2: /scratch/stefan/7770410/working/building/REAL300020113476/2.* 1: /scratch/stefan/7770410/working/building/REAL300020113476/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113476/0.* 3: /scratch/stefan/7770410/working/building/REAL300020113476/3.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113476 Building REAL300020113477 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113477' /scratch/stefan/7770410/working/building/REAL300020113477 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113477 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113477/0 /scratch/stefan/7770410/working/building/REAL300020113477 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/558 `/scratch/stefan/7770410/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)NC=N1) `REAL300020113477.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113477 none CC(C)(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 41, 60, 68, 68, 68, 68, 12, 12, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 12, 41, 41, 60, 60, 1, 1, 11, 11] 201 rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 47, 48, 40, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50]) total number of confs: 285 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113477 none CC(C)(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 80, 80, 45, 45, 45, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 12, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 45, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 80, 80] 201 rigid atoms, others: [42, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 228 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113477 none CC(C)(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 11, 11, 11, 80, 80, 80, 157, 201, 201, 201, 201, 201, 80, 80, 11, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 11, 11, 11, 11, 80, 157, 157, 201, 201, 11, 11, 1, 1] 201 rigid atoms, others: [1, 4, 5, 6, 49, 50, 25, 26, 27] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 772 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113477 none CC(C)(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 139, 139, 139, 68, 68, 68, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 68, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 139, 68, 68, 68, 68, 14, 6, 6, 4, 4, 68, 68, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 521 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113477 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113477/1 /scratch/stefan/7770410/working/building/REAL300020113477 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 559) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/559 `/scratch/stefan/7770410/working/3D/559' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)NC=N1) `REAL300020113477.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113477 none CC(C)(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 41, 60, 68, 68, 68, 68, 12, 12, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 12, 41, 41, 60, 60, 1, 1, 11, 11] 201 rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 47, 48, 40, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50]) total number of confs: 285 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113477 none CC(C)(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 80, 80, 45, 45, 45, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 12, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 45, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 80, 80] 201 rigid atoms, others: [42, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 228 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113477 none CC(C)(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 11, 11, 11, 80, 80, 80, 157, 201, 201, 201, 201, 201, 80, 80, 11, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 11, 11, 11, 11, 80, 157, 157, 201, 201, 11, 11, 1, 1] 201 rigid atoms, others: [1, 4, 5, 6, 49, 50, 25, 26, 27] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 772 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113477 none CC(C)(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 139, 139, 139, 68, 68, 68, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 68, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 139, 68, 68, 68, 68, 14, 6, 6, 4, 4, 68, 68, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 521 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113477 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113477 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113477/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113477/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113477 Building REAL300020113478 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113478' /scratch/stefan/7770410/working/building/REAL300020113478 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113478 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113478/0 /scratch/stefan/7770410/working/building/REAL300020113478 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/560 `/scratch/stefan/7770410/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C[C@@H]1C[C@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113478.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113478 none CC(C)(C)C[C@@H]1C[C@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 65, 39, 39, 39, 39, 6, 39, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 21, 28, 28, 28, 28, 28, 12, 12, 1, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 39, 39, 6, 1, 1, 1, 1, 12, 21, 21, 28, 28, 1, 1] 201 rigid atoms, others: [45, 44, 43, 12, 13, 14, 15, 16, 52, 46, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 341 number of broken/clashed sets: 190 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113478 none CC(C)(C)C[C@@H]1C[C@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [168, 168, 168, 168, 126, 126, 126, 126, 39, 126, 39, 39, 12, 12, 12, 1, 1, 1, 1, 1, 4, 6, 6, 6, 6, 6, 1, 1, 12, 168, 168, 168, 168, 168, 168, 168, 168, 168, 168, 168, 126, 126, 39, 12, 12, 12, 12, 1, 4, 4, 6, 6, 12, 12] 201 rigid atoms, others: [15, 47, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 611 number of broken/clashed sets: 190 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113478 none CC(C)(C)C[C@@H]1C[C@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 39, 39, 39, 126, 126, 126, 141, 153, 153, 153, 153, 153, 126, 126, 39, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 11, 39, 39, 39, 39, 126, 141, 141, 153, 153, 39, 39] 201 rigid atoms, others: [4, 5, 6, 7, 8, 41, 10, 40, 9] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 392 number of broken/clashed sets: 190 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113478 none CC(C)(C)C[C@@H]1C[C@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 157, 157, 157, 157, 77, 157, 77, 77, 30, 30, 30, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 30, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 157, 157, 77, 30, 30, 30, 30, 7, 4, 4, 2, 2, 30, 30] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 732 number of broken/clashed sets: 192 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113478 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113478/1 /scratch/stefan/7770410/working/building/REAL300020113478 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 561) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/561 `/scratch/stefan/7770410/working/3D/561' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C[C@@H]1C[C@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113478.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113478 none CC(C)(C)C[C@@H]1C[C@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 65, 39, 39, 39, 39, 6, 39, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 21, 28, 28, 28, 28, 28, 12, 12, 1, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 39, 39, 6, 1, 1, 1, 1, 12, 21, 21, 28, 28, 1, 1] 201 rigid atoms, others: [45, 44, 43, 12, 13, 14, 15, 16, 52, 46, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 341 number of broken/clashed sets: 190 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113478 none CC(C)(C)C[C@@H]1C[C@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 169, 169, 126, 126, 126, 126, 39, 126, 39, 39, 12, 12, 12, 1, 1, 1, 1, 1, 4, 6, 6, 6, 6, 6, 1, 1, 12, 169, 169, 169, 169, 169, 169, 169, 169, 169, 169, 169, 126, 126, 39, 12, 12, 12, 12, 1, 4, 4, 6, 6, 12, 12] 201 rigid atoms, others: [15, 47, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 617 number of broken/clashed sets: 190 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113478 none CC(C)(C)C[C@@H]1C[C@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 39, 39, 39, 126, 126, 126, 141, 153, 153, 153, 153, 153, 126, 126, 39, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 11, 39, 39, 39, 39, 126, 141, 141, 153, 153, 39, 39] 201 rigid atoms, others: [4, 5, 6, 7, 8, 41, 10, 40, 9] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 392 number of broken/clashed sets: 190 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113478 none CC(C)(C)C[C@@H]1C[C@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 158, 158, 158, 158, 78, 158, 78, 78, 31, 31, 31, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 31, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 158, 158, 78, 31, 31, 31, 31, 8, 4, 4, 2, 2, 31, 31] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 730 number of broken/clashed sets: 191 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113478 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113478 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113478/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113478/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113478 Building REAL300020113479 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113479' /scratch/stefan/7770410/working/building/REAL300020113479 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300020113479 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113479/0 /scratch/stefan/7770410/working/building/REAL300020113479 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/562 `/scratch/stefan/7770410/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC=CN1C(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113479.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113479 none CCC1=NC=CN1C(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 45, 45, 45, 45, 45, 31, 18, 31, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 20, 30, 30, 30, 30, 30, 8, 8, 1, 64, 64, 64, 64, 64, 45, 45, 31, 31, 31, 31, 18, 18, 5, 1, 1, 1, 1, 8, 20, 20, 30, 30, 1, 1] 201 rigid atoms, others: [45, 44, 43, 12, 13, 14, 15, 16, 52, 46, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 389 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113479 none CCC1=NC=CN1C(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [150, 126, 126, 126, 126, 126, 93, 71, 93, 21, 21, 21, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 150, 150, 150, 150, 150, 126, 126, 93, 93, 93, 93, 71, 71, 21, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [15, 47, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 608 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113479 none CCC1=NC=CN1C(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 22, 22, 22, 45, 45, 45, 126, 126, 126, 169, 200, 200, 200, 200, 200, 126, 126, 45, 6, 6, 6, 5, 5, 1, 1, 3, 4, 4, 4, 9, 9, 22, 45, 45, 45, 45, 126, 169, 169, 200, 200, 45, 45] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 34, 35] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 704 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113479 none CCC1=NC=CN1C(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 195, 172, 195, 69, 69, 69, 46, 46, 46, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 46, 201, 201, 201, 201, 201, 201, 201, 195, 195, 195, 195, 172, 172, 69, 46, 46, 46, 46, 11, 6, 6, 4, 4, 46, 46] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 788 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113479 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113479/1 /scratch/stefan/7770410/working/building/REAL300020113479 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 563) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/563 `/scratch/stefan/7770410/working/3D/563' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC=CN1C(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113479.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113479 none CCC1=NC=CN1C(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 45, 45, 45, 45, 45, 31, 18, 31, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 20, 30, 30, 30, 30, 30, 8, 8, 1, 64, 64, 64, 64, 64, 45, 45, 31, 31, 31, 31, 18, 18, 5, 1, 1, 1, 1, 8, 20, 20, 30, 30, 1, 1] 201 rigid atoms, others: [45, 44, 43, 12, 13, 14, 15, 16, 52, 46, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 389 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113479 none CCC1=NC=CN1C(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [149, 125, 125, 125, 125, 125, 93, 71, 93, 21, 21, 21, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 149, 149, 149, 149, 149, 125, 125, 93, 93, 93, 93, 71, 71, 21, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [15, 47, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 606 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113479 none CCC1=NC=CN1C(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 22, 22, 22, 45, 45, 45, 125, 125, 125, 168, 200, 200, 200, 200, 200, 125, 125, 45, 6, 6, 6, 5, 5, 1, 1, 3, 4, 4, 4, 9, 9, 22, 45, 45, 45, 45, 125, 168, 168, 200, 200, 45, 45] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 34, 35] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 709 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113479 none CCC1=NC=CN1C(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 195, 172, 195, 69, 69, 69, 46, 46, 46, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 46, 201, 201, 201, 201, 201, 201, 201, 195, 195, 195, 195, 172, 172, 69, 46, 46, 46, 46, 11, 6, 6, 4, 4, 46, 46] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 788 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113479 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `2' /scratch/stefan/7770410/working/building/REAL300020113479/2 /scratch/stefan/7770410/working/building/REAL300020113479 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 2 (index: 564) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/564 `/scratch/stefan/7770410/working/3D/564' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=[NH+]C=CN1C(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113479.mol2' -> `2.mol2' `temp.mol2' -> `REAL300020113479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113479/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113479 none CCC1=[NH+]C=CN1C(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 6, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [57, 47, 47, 47, 47, 47, 47, 28, 20, 28, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 16, 24, 24, 24, 24, 24, 7, 7, 1, 57, 57, 57, 57, 57, 47, 47, 28, 28, 28, 28, 20, 20, 5, 1, 1, 1, 1, 7, 16, 16, 24, 24, 1, 1] 110 rigid atoms, others: [45, 44, 13, 14, 15, 16, 17, 46, 54, 47, 29, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50, 51, 52]) total number of confs: 301 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113479 none CCC1=[NH+]C=CN1C(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 6, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [90, 84, 84, 84, 84, 84, 84, 60, 48, 60, 16, 16, 16, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 90, 90, 90, 90, 90, 84, 84, 60, 60, 60, 60, 48, 48, 16, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 110 rigid atoms, others: [48, 16, 17, 18, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54]) total number of confs: 350 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113479 none CCC1=[NH+]C=CN1C(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 6, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 23, 23, 23, 47, 47, 47, 84, 84, 84, 102, 108, 108, 108, 108, 108, 84, 84, 47, 6, 6, 6, 6, 6, 1, 1, 6, 6, 6, 6, 9, 9, 23, 47, 47, 47, 47, 84, 102, 102, 108, 108, 47, 47] 110 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 35, 36] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 365 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113479 none CCC1=[NH+]C=CN1C(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 6, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 6, 3, 3, 3, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 3, 3, 3, 3, 2, 2, 2, 1, 1, 3, 3] 7 rigid atoms, others: [25, 51, 52, 21, 22, 23, 24, 20, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 53, 54]) total number of confs: 27 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113479 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113479 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 2: /scratch/stefan/7770410/working/building/REAL300020113479/2.* 1: /scratch/stefan/7770410/working/building/REAL300020113479/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113479/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113479 Building REAL300020113480 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113480' /scratch/stefan/7770410/working/building/REAL300020113480 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113480 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113480/0 /scratch/stefan/7770410/working/building/REAL300020113480 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/565 `/scratch/stefan/7770410/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=CSC2=NC=N1) `REAL300020113480.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113480 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=CSC2=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 14, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 4, 4, 4, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 4, 9, 19, 19, 19, 19, 19, 19, 19, 19, 9, 4, 4, 4, 4, 1, 5, 5, 5, 5, 4, 4, 19, 19, 19] 23 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113480 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=CSC2=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 14, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 7, 7, 7, 6, 6, 6, 4, 2, 1, 1, 1, 1, 1, 1, 6, 6, 7, 15, 23, 23, 23, 23, 23, 23, 23, 23, 15, 7, 7, 7, 7, 6, 4, 4, 2, 2, 7, 7, 23, 23, 23] 23 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 62 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113480 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=CSC2=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 14, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 6, 4, 4, 1, 6, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 4, 6, 6, 6, 6, 1, 1, 19, 19, 19] 23 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113480 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=CSC2=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 14, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 19, 19, 19, 19, 19, 19, 23, 23, 23, 23, 23, 23, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 19, 19, 19, 19, 19, 23, 23, 23, 23, 19, 19, 1, 1, 1] 23 rigid atoms, others: [1, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 71 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113480 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113480/1 /scratch/stefan/7770410/working/building/REAL300020113480 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 566) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/566 `/scratch/stefan/7770410/working/3D/566' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=CSC2=NC=N1) `REAL300020113480.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113480/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113480 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=CSC2=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 14, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 4, 4, 4, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 4, 9, 19, 19, 19, 19, 19, 19, 19, 19, 9, 4, 4, 4, 4, 1, 5, 5, 5, 5, 4, 4, 19, 19, 19] 23 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113480 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=CSC2=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 14, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 6, 6, 6, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 14, 23, 23, 23, 23, 23, 23, 23, 23, 14, 6, 6, 6, 6, 5, 3, 3, 1, 1, 6, 6, 23, 23, 23] 23 rigid atoms, others: [36, 37, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42]) total number of confs: 58 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113480 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=CSC2=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 14, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 6, 4, 4, 1, 6, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 4, 6, 6, 6, 6, 1, 1, 19, 19, 19] 23 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113480 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=CSC2=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 14, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 19, 19, 19, 19, 19, 19, 23, 23, 23, 23, 23, 23, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 19, 19, 19, 19, 19, 23, 23, 23, 23, 19, 19, 1, 1, 1] 23 rigid atoms, others: [1, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 71 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113480 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113480 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113480/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113480/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113480 Building REAL300020113481 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113481' /scratch/stefan/7770410/working/building/REAL300020113481 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113481 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113481/0 /scratch/stefan/7770410/working/building/REAL300020113481 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/567 `/scratch/stefan/7770410/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=NN(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1) `REAL300020113481.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113481 none NC(=O)C1=NN(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 32, 42, 32, 32, 23, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 22, 34, 34, 34, 34, 34, 9, 9, 1, 32, 32, 42, 42, 23, 23, 5, 1, 1, 1, 1, 9, 22, 22, 34, 34, 1, 1, 32] 201 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 273 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113481 none NC(=O)C1=NN(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 103, 127, 103, 103, 82, 25, 25, 25, 9, 9, 9, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 9, 103, 103, 127, 127, 82, 82, 25, 9, 9, 9, 9, 1, 5, 5, 7, 7, 9, 9, 103] 201 rigid atoms, others: [37, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 453 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113481 none NC(=O)C1=NN(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 5, 13, 13, 13, 32, 32, 32, 103, 103, 103, 151, 174, 174, 174, 174, 174, 103, 103, 32, 1, 1, 3, 3, 5, 5, 13, 32, 32, 32, 32, 103, 151, 151, 174, 174, 32, 32, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 44, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 593 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113481 none NC(=O)C1=NN(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 172, 201, 172, 172, 157, 68, 68, 68, 35, 35, 35, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 35, 172, 172, 201, 201, 157, 157, 68, 35, 35, 35, 35, 7, 4, 4, 2, 2, 35, 35, 172] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 745 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113481 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113481/1 /scratch/stefan/7770410/working/building/REAL300020113481 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 568) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/568 `/scratch/stefan/7770410/working/3D/568' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=NN(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1) `REAL300020113481.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113481 none NC(=O)C1=NN(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 32, 42, 32, 32, 23, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 23, 35, 35, 35, 35, 35, 9, 9, 1, 32, 32, 42, 42, 23, 23, 5, 1, 1, 1, 1, 9, 23, 23, 35, 35, 1, 1, 32] 201 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 276 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113481 none NC(=O)C1=NN(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 103, 127, 103, 103, 82, 25, 25, 25, 9, 9, 9, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 9, 103, 103, 127, 127, 82, 82, 25, 9, 9, 9, 9, 1, 5, 5, 7, 7, 9, 9, 103] 201 rigid atoms, others: [37, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 453 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113481 none NC(=O)C1=NN(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 5, 13, 13, 13, 32, 32, 32, 103, 103, 103, 152, 175, 175, 175, 175, 175, 103, 103, 32, 1, 1, 3, 3, 5, 5, 13, 32, 32, 32, 32, 103, 152, 152, 175, 175, 32, 32, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 44, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 596 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113481 none NC(=O)C1=NN(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 173, 201, 173, 173, 158, 68, 68, 68, 35, 35, 35, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 35, 173, 173, 201, 201, 158, 158, 68, 35, 35, 35, 35, 7, 4, 4, 2, 2, 35, 35, 173] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 747 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113481 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113481 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113481/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113481/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113481 Building REAL300020113482 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113482' /scratch/stefan/7770410/working/building/REAL300020113482 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for REAL300020113482 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113482/0 /scratch/stefan/7770410/working/building/REAL300020113482 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/569 `/scratch/stefan/7770410/working/3D/569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC[N@@H+]1C) `REAL300020113482.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113482 none CC[C@@H]1[C@@H](C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 6, 16, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 11, 11, 11, 11, 11, 11, 9, 9, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 9, 11, 11, 11, 11, 1, 1, 16, 16, 16, 16, 16, 16, 16] 46 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 45, 46, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 64 number of broken/clashed sets: 46 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113482 none CC[C@@H]1[C@@H](C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 32, 45, 32, 32, 9, 9, 9, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 9, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 32, 9, 9, 9, 9, 1, 4, 4, 4, 4, 9, 9, 45, 45, 45, 45, 45, 45, 45] 46 rigid atoms, others: [40, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 141 number of broken/clashed sets: 46 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113482 none CC[C@@H]1[C@@H](C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 45, 45, 45, 46, 46, 46, 46, 46, 46, 45, 45, 16, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 16, 16, 16, 16, 45, 46, 46, 46, 46, 16, 16, 1, 1, 1, 1, 2, 2, 2] 46 rigid atoms, others: [1, 2, 3, 4, 5, 6, 47, 48, 49, 50, 25, 26, 27, 28, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52, 53]) total number of confs: 100 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113482 none CC[C@@H]1[C@@H](C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 34, 46, 34, 34, 11, 11, 11, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 34, 11, 11, 11, 11, 4, 3, 3, 1, 1, 11, 11, 46, 46, 46, 46, 46, 46, 46] 46 rigid atoms, others: [43, 44, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 138 number of broken/clashed sets: 46 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113482 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113482/1 /scratch/stefan/7770410/working/building/REAL300020113482 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 570) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/570 `/scratch/stefan/7770410/working/3D/570' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC[N@H+]1C) `REAL300020113482.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113482 none CC[C@@H]1[C@@H](C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 34, 34, 34, 6, 34, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 26, 26, 26, 26, 26, 26, 13, 13, 1, 34, 34, 34, 34, 34, 65, 65, 65, 65, 65, 6, 1, 1, 1, 1, 13, 26, 26, 26, 26, 1, 1, 34, 34, 34, 34, 34, 34, 34] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 45, 46, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 317 number of broken/clashed sets: 83 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113482 none CC[C@@H]1[C@@H](C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [176, 152, 152, 152, 55, 152, 55, 55, 13, 13, 13, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 13, 152, 152, 152, 152, 152, 176, 176, 176, 176, 176, 55, 13, 13, 13, 13, 1, 4, 4, 4, 4, 13, 13, 152, 152, 152, 152, 152, 152, 152] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 565 number of broken/clashed sets: 83 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113482 none CC[C@@H]1[C@@H](C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 34, 34, 34, 152, 152, 152, 201, 201, 201, 201, 201, 201, 152, 152, 34, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 10, 34, 34, 34, 34, 152, 201, 201, 201, 201, 34, 34, 1, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 47, 48, 49, 50, 25, 26, 27, 28, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52, 53]) total number of confs: 537 number of broken/clashed sets: 83 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113482 none CC[C@@H]1[C@@H](C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 90, 201, 90, 90, 25, 25, 25, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 25, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 90, 25, 25, 25, 25, 3, 3, 3, 1, 1, 25, 25, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [43, 44, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 566 number of broken/clashed sets: 91 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113482 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `2' /scratch/stefan/7770410/working/building/REAL300020113482/2 /scratch/stefan/7770410/working/building/REAL300020113482 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 2 (index: 571) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/571 `/scratch/stefan/7770410/working/3D/571' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC[N@@H+]1C) `REAL300020113482.mol2' -> `2.mol2' `temp.mol2' -> `REAL300020113482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113482/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113482 none CC[C@@H]1[C@@H](C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 6, 16, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 11, 11, 11, 11, 11, 11, 9, 9, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 9, 11, 11, 11, 11, 1, 1, 16, 16, 16, 16, 16, 16, 16] 46 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 45, 46, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 64 number of broken/clashed sets: 46 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113482 none CC[C@@H]1[C@@H](C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 32, 45, 32, 32, 9, 9, 9, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 9, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 32, 9, 9, 9, 9, 1, 4, 4, 4, 4, 9, 9, 45, 45, 45, 45, 45, 45, 45] 46 rigid atoms, others: [40, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 141 number of broken/clashed sets: 46 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113482 none CC[C@@H]1[C@@H](C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 45, 45, 45, 46, 46, 46, 46, 46, 46, 45, 45, 16, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 16, 16, 16, 16, 45, 46, 46, 46, 46, 16, 16, 1, 1, 1, 1, 2, 2, 2] 46 rigid atoms, others: [1, 2, 3, 4, 5, 6, 47, 48, 49, 50, 25, 26, 27, 28, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52, 53]) total number of confs: 100 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113482 none CC[C@@H]1[C@@H](C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 35, 46, 35, 35, 12, 12, 12, 5, 5, 5, 4, 2, 1, 1, 1, 1, 1, 1, 5, 5, 12, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 35, 12, 12, 12, 12, 5, 4, 4, 2, 2, 12, 12, 46, 46, 46, 46, 46, 46, 46] 46 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 142 number of broken/clashed sets: 46 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113482 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `3' /scratch/stefan/7770410/working/building/REAL300020113482/3 /scratch/stefan/7770410/working/building/REAL300020113482 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 3 (index: 572) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/572 `/scratch/stefan/7770410/working/3D/572' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC[N@H+]1C) `REAL300020113482.mol2' -> `3.mol2' `temp.mol2' -> `REAL300020113482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113482/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113482 none CC[C@@H]1[C@@H](C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 34, 34, 34, 6, 34, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 26, 26, 26, 26, 26, 26, 13, 13, 1, 34, 34, 34, 34, 34, 65, 65, 65, 65, 65, 6, 1, 1, 1, 1, 13, 26, 26, 26, 26, 1, 1, 34, 34, 34, 34, 34, 34, 34] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 45, 46, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 317 number of broken/clashed sets: 83 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113482 none CC[C@@H]1[C@@H](C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [176, 152, 152, 152, 55, 152, 55, 55, 13, 13, 13, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 13, 152, 152, 152, 152, 152, 176, 176, 176, 176, 176, 55, 13, 13, 13, 13, 1, 4, 4, 4, 4, 13, 13, 152, 152, 152, 152, 152, 152, 152] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 565 number of broken/clashed sets: 83 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113482 none CC[C@@H]1[C@@H](C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 34, 34, 34, 152, 152, 152, 201, 201, 201, 201, 201, 201, 152, 152, 34, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 10, 34, 34, 34, 34, 152, 201, 201, 201, 201, 34, 34, 1, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 47, 48, 49, 50, 25, 26, 27, 28, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52, 53]) total number of confs: 537 number of broken/clashed sets: 83 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113482 none CC[C@@H]1[C@@H](C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 90, 201, 90, 90, 25, 25, 25, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 25, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 90, 25, 25, 25, 25, 3, 3, 3, 1, 1, 25, 25, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [43, 44, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 566 number of broken/clashed sets: 91 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113482 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113482 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 2: /scratch/stefan/7770410/working/building/REAL300020113482/2.* 1: /scratch/stefan/7770410/working/building/REAL300020113482/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113482/0.* 3: /scratch/stefan/7770410/working/building/REAL300020113482/3.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113482 Building REAL300020113483 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113483' /scratch/stefan/7770410/working/building/REAL300020113483 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113483 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113483/0 /scratch/stefan/7770410/working/building/REAL300020113483 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/573 `/scratch/stefan/7770410/working/3D/573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@@H]2C=C[C@H]1CC2) `REAL300020113483.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113483 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@@H]2C=C[C@H]1CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 5, 7, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 41, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 41, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 100, 100, 100, 100, 100, 100, 100, 100] 201 rigid atoms, others: [35, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 310 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113483 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@@H]2C=C[C@H]1CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 5, 7, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 60, 60, 60, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 60, 127, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 127, 60, 60, 60, 60, 11, 6, 6, 4, 4, 60, 60, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 605 number of broken/clashed sets: 21 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113483 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@@H]2C=C[C@H]1CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 5, 7, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 35, 53, 60, 60, 60, 60, 11, 11, 1, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 1, 1, 1, 1, 11, 35, 35, 53, 53, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 40, 41, 34, 18, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 299 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113483 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@@H]2C=C[C@H]1CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 5, 7, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 28, 28, 28, 100, 100, 100, 173, 201, 201, 201, 201, 201, 100, 100, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 28, 28, 28, 28, 100, 173, 173, 201, 201, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 692 number of broken/clashed sets: 21 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113483 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113483/1 /scratch/stefan/7770410/working/building/REAL300020113483 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 574) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/574 `/scratch/stefan/7770410/working/3D/574' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@@H]2C=C[C@H]1CC2) `REAL300020113483.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113483/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113483 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@@H]2C=C[C@H]1CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 5, 7, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 41, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 41, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 100, 100, 100, 100, 100, 100, 100, 100] 201 rigid atoms, others: [35, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 310 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113483 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@@H]2C=C[C@H]1CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 5, 7, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 60, 60, 60, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 60, 127, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 127, 60, 60, 60, 60, 11, 6, 6, 4, 4, 60, 60, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 605 number of broken/clashed sets: 21 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113483 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@@H]2C=C[C@H]1CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 5, 7, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 35, 53, 60, 60, 60, 60, 11, 11, 1, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 1, 1, 1, 1, 11, 35, 35, 53, 53, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 40, 41, 34, 18, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 299 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113483 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@@H]2C=C[C@H]1CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 5, 7, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 28, 28, 28, 100, 100, 100, 173, 201, 201, 201, 201, 201, 100, 100, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 28, 28, 28, 28, 100, 173, 173, 201, 201, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 692 number of broken/clashed sets: 21 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113483 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113483 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113483/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113483/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113483 Building REAL300020113484 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113484' /scratch/stefan/7770410/working/building/REAL300020113484 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113484 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113484/0 /scratch/stefan/7770410/working/building/REAL300020113484 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 575) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/575 `/scratch/stefan/7770410/working/3D/575' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=CC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1) `REAL300020113484.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113484 none CCN1C=CC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 15, 15, 15, 15, 15, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 18, 30, 30, 30, 30, 30, 7, 7, 1, 15, 35, 35, 35, 35, 35, 15, 15, 15, 15, 5, 1, 1, 1, 1, 7, 18, 18, 30, 30, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 276 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113484 none CCN1C=CC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 59, 59, 59, 59, 59, 18, 18, 18, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 59, 108, 108, 108, 108, 108, 59, 59, 59, 59, 18, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 514 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113484 none CCN1C=CC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 15, 15, 15, 59, 59, 59, 96, 117, 117, 117, 117, 117, 59, 59, 15, 1, 5, 5, 5, 5, 5, 1, 1, 3, 3, 7, 15, 15, 15, 15, 59, 96, 96, 117, 117, 15, 15] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 437 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113484 none CCN1C=CC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 117, 117, 117, 117, 117, 49, 49, 49, 30, 30, 30, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 30, 117, 201, 201, 201, 201, 201, 117, 117, 117, 117, 49, 30, 30, 30, 30, 7, 4, 4, 2, 2, 30, 30] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 943 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113484 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113484/1 /scratch/stefan/7770410/working/building/REAL300020113484 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 576) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/576 `/scratch/stefan/7770410/working/3D/576' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=CC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1) `REAL300020113484.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113484 none CCN1C=CC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 15, 15, 15, 15, 15, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 18, 30, 30, 30, 30, 30, 7, 7, 1, 15, 34, 34, 34, 34, 34, 15, 15, 15, 15, 5, 1, 1, 1, 1, 7, 18, 18, 30, 30, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 273 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113484 none CCN1C=CC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 57, 57, 57, 57, 57, 18, 18, 18, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 57, 107, 107, 107, 107, 107, 57, 57, 57, 57, 18, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 514 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113484 none CCN1C=CC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 15, 15, 15, 57, 57, 57, 94, 116, 116, 116, 116, 116, 57, 57, 15, 1, 5, 5, 5, 5, 5, 1, 1, 3, 3, 7, 15, 15, 15, 15, 57, 94, 94, 116, 116, 15, 15] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 441 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113484 none CCN1C=CC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 116, 116, 116, 116, 116, 49, 49, 49, 30, 30, 30, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 30, 116, 201, 201, 201, 201, 201, 116, 116, 116, 116, 49, 30, 30, 30, 30, 7, 4, 4, 2, 2, 30, 30] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 946 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113484 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113484 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113484/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113484/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113484 Building REAL300020113485 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113485' /scratch/stefan/7770410/working/building/REAL300020113485 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113485 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113485/0 /scratch/stefan/7770410/working/building/REAL300020113485 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/577 `/scratch/stefan/7770410/working/3D/577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C2CCC2)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113485.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113485 none CN1N=CC(C2CCC2)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 16, 16, 16, 36, 36, 36, 72, 72, 72, 101, 121, 121, 121, 121, 121, 72, 72, 36, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 16, 36, 36, 36, 36, 72, 101, 101, 121, 121, 36, 36] 121 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 39, 36, 38, 37] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 431 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113485 none CN1N=CC(C2CCC2)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 96, 96, 96, 120, 120, 120, 65, 65, 65, 29, 29, 29, 11, 11, 11, 7, 3, 1, 1, 1, 1, 1, 1, 11, 11, 29, 96, 96, 96, 96, 120, 120, 120, 120, 120, 120, 120, 65, 29, 29, 29, 29, 11, 7, 7, 3, 3, 29, 29] 120 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 342 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113485 none CN1N=CC(C2CCC2)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 22, 22, 36, 36, 36, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 17, 25, 26, 26, 26, 26, 6, 6, 1, 22, 22, 22, 22, 36, 36, 36, 36, 36, 36, 36, 6, 1, 1, 1, 1, 6, 17, 17, 25, 25, 1, 1] 121 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 189 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113485 none CN1N=CC(C2CCC2)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 8, 8, 22, 22, 22, 55, 55, 55, 79, 96, 96, 96, 96, 96, 55, 55, 22, 2, 2, 2, 1, 5, 5, 5, 5, 5, 5, 5, 8, 22, 22, 22, 22, 55, 79, 79, 96, 96, 22, 22] 121 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 9, 10] set([6, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 350 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113485 none CN1N=CC(C2CCC2)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 55, 55, 55, 72, 72, 72, 23, 23, 23, 6, 6, 6, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 6, 55, 55, 55, 55, 72, 72, 72, 72, 72, 72, 72, 23, 6, 6, 6, 6, 1, 6, 6, 8, 8, 6, 6] 121 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 206 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113485 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113485/1 /scratch/stefan/7770410/working/building/REAL300020113485 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 578) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/578 `/scratch/stefan/7770410/working/3D/578' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C2CCC2)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113485.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113485/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113485 none CN1N=CC(C2CCC2)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 16, 16, 16, 36, 36, 36, 73, 73, 73, 101, 122, 122, 122, 122, 122, 73, 73, 36, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 16, 36, 36, 36, 36, 73, 101, 101, 122, 122, 36, 36] 122 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 39, 36, 38, 37] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 435 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113485 none CN1N=CC(C2CCC2)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 96, 96, 96, 122, 122, 122, 65, 65, 65, 29, 29, 29, 11, 11, 11, 7, 3, 1, 1, 1, 1, 1, 1, 11, 11, 29, 96, 96, 96, 96, 122, 122, 122, 122, 122, 122, 122, 65, 29, 29, 29, 29, 11, 7, 7, 3, 3, 29, 29] 122 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 350 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113485 none CN1N=CC(C2CCC2)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 22, 22, 36, 36, 36, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 17, 25, 26, 26, 26, 26, 6, 6, 1, 22, 22, 22, 22, 36, 36, 36, 36, 36, 36, 36, 6, 1, 1, 1, 1, 6, 17, 17, 25, 25, 1, 1] 122 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 189 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113485 none CN1N=CC(C2CCC2)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 8, 8, 22, 22, 22, 55, 55, 55, 78, 95, 95, 95, 95, 95, 55, 55, 22, 2, 2, 2, 1, 5, 5, 5, 5, 5, 5, 5, 8, 22, 22, 22, 22, 55, 78, 78, 95, 95, 22, 22] 122 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 9, 10] set([6, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 347 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113485 none CN1N=CC(C2CCC2)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 55, 55, 55, 73, 73, 73, 23, 23, 23, 6, 6, 6, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 6, 55, 55, 55, 55, 73, 73, 73, 73, 73, 73, 73, 23, 6, 6, 6, 6, 1, 6, 6, 8, 8, 6, 6] 122 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 210 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113485 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113485 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113485/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113485/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113485 Building REAL300020113486 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113486' /scratch/stefan/7770410/working/building/REAL300020113486 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113486 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113486/0 /scratch/stefan/7770410/working/building/REAL300020113486 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/579 `/scratch/stefan/7770410/working/3D/579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@]12C[C@H]1COC2) `REAL300020113486.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113486 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@]12C[C@H]1COC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 5, 12, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 11, 36, 79, 79, 79, 79, 79, 79, 36, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 79, 79, 79, 79, 79, 79] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 200 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113486 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@]12C[C@H]1COC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 5, 12, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 69, 69, 69, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 69, 114, 201, 201, 201, 201, 201, 201, 114, 69, 69, 69, 69, 13, 6, 6, 4, 4, 69, 69, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 469 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113486 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@]12C[C@H]1COC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 5, 12, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 42, 58, 69, 69, 69, 69, 11, 11, 1, 6, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 11, 42, 42, 58, 58, 1, 1, 18, 18, 18, 18, 18, 18] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113486 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@]12C[C@H]1COC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 5, 12, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 18, 18, 18, 79, 79, 79, 161, 201, 201, 201, 201, 201, 79, 79, 18, 1, 1, 1, 1, 1, 1, 1, 6, 18, 18, 18, 18, 79, 161, 161, 201, 201, 18, 18, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 38, 39, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 765 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113486 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113486/1 /scratch/stefan/7770410/working/building/REAL300020113486 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 580) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/580 `/scratch/stefan/7770410/working/3D/580' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@]12C[C@H]1COC2) `REAL300020113486.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113486/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113486 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@]12C[C@H]1COC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 5, 12, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 11, 37, 80, 80, 80, 80, 80, 80, 37, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 80, 80, 80, 80, 80, 80] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 202 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113486 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@]12C[C@H]1COC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 5, 12, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 72, 72, 72, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 72, 118, 201, 201, 201, 201, 201, 201, 118, 72, 72, 72, 72, 14, 6, 6, 4, 4, 72, 72, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 469 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113486 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@]12C[C@H]1COC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 5, 12, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 41, 57, 68, 68, 68, 68, 11, 11, 1, 6, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 11, 41, 41, 57, 57, 1, 1, 18, 18, 18, 18, 18, 18] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43]) total number of confs: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113486 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@]12C[C@H]1COC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 5, 12, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 18, 18, 18, 80, 80, 80, 161, 201, 201, 201, 201, 201, 80, 80, 18, 1, 1, 1, 1, 1, 1, 1, 6, 18, 18, 18, 18, 80, 161, 161, 201, 201, 18, 18, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 38, 39, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 763 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113486 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113486 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113486/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113486/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113486 Building REAL300020113487 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113487' /scratch/stefan/7770410/working/building/REAL300020113487 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113487 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113487/0 /scratch/stefan/7770410/working/building/REAL300020113487 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/581 `/scratch/stefan/7770410/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2N=CNC2=CN=C1) `REAL300020113487.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113487 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2N=CNC2=CN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 12, 12, 12, 1, 1, 1, 1, 1, 9, 13, 21, 21, 21, 21, 1, 1, 12, 51, 80, 80, 80, 80, 80, 80, 80, 80, 51, 12, 12, 12, 12, 1, 9, 9, 13, 13, 12, 12, 80, 80, 80, 80] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 245 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113487 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2N=CNC2=CN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [198, 198, 112, 112, 112, 26, 26, 26, 6, 4, 1, 1, 1, 1, 1, 1, 26, 26, 112, 198, 201, 201, 201, 201, 201, 201, 201, 201, 198, 112, 112, 112, 112, 26, 6, 6, 4, 4, 112, 112, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 546 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113487 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2N=CNC2=CN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 70, 92, 114, 114, 114, 114, 12, 12, 1, 6, 13, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 12, 70, 70, 92, 92, 1, 1, 13, 13, 13, 13] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 420 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113487 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2N=CNC2=CN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 13, 13, 13, 80, 80, 80, 174, 201, 201, 201, 201, 201, 80, 80, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 13, 13, 13, 13, 80, 174, 174, 201, 201, 13, 13, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 721 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113487 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113487/1 /scratch/stefan/7770410/working/building/REAL300020113487 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 582) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/582 `/scratch/stefan/7770410/working/3D/582' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2N=CNC2=CN=C1) `REAL300020113487.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113487/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113487 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2N=CNC2=CN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 12, 12, 12, 1, 1, 1, 1, 1, 9, 13, 21, 21, 21, 21, 1, 1, 12, 51, 80, 80, 80, 80, 80, 80, 80, 80, 51, 12, 12, 12, 12, 1, 9, 9, 13, 13, 12, 12, 80, 80, 80, 80] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 245 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113487 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2N=CNC2=CN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 199, 115, 115, 115, 26, 26, 26, 6, 4, 1, 1, 1, 1, 1, 1, 26, 26, 115, 199, 201, 201, 201, 201, 201, 201, 201, 201, 199, 115, 115, 115, 115, 26, 6, 6, 4, 4, 115, 115, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 546 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113487 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2N=CNC2=CN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 70, 92, 114, 114, 114, 114, 12, 12, 1, 6, 13, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 12, 70, 70, 92, 92, 1, 1, 13, 13, 13, 13] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 420 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113487 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2N=CNC2=CN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 13, 13, 13, 80, 80, 80, 174, 201, 201, 201, 201, 201, 80, 80, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 13, 13, 13, 13, 80, 174, 174, 201, 201, 13, 13, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 721 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113487 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113487 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113487/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113487/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113487 Building REAL300020113488 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113488' /scratch/stefan/7770410/working/building/REAL300020113488 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113488 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113488/0 /scratch/stefan/7770410/working/building/REAL300020113488 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 583) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/583 `/scratch/stefan/7770410/working/3D/583' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCC2=NC=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)N21) `REAL300020113488.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113488 none CC1CCCC2=NC=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)N21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 50, 70, 81, 81, 81, 81, 13, 13, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 13, 50, 50, 70, 70, 1, 1] 201 rigid atoms, others: [43, 41, 42, 11, 12, 13, 14, 15, 50, 51, 27, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 325 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113488 none CC1CCCC2=NC=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)N21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 89, 89, 89, 89, 89, 50, 50, 50, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 13, 89, 89, 89, 89, 89, 89, 89, 89, 89, 89, 89, 89, 50, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13] 201 rigid atoms, others: [45, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 231 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113488 none CC1CCCC2=NC=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)N21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 89, 89, 89, 157, 201, 201, 201, 201, 201, 89, 89, 14, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 14, 14, 14, 14, 89, 157, 157, 201, 201, 14, 14] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 8, 9, 7, 34, 35, 36, 6, 28, 37, 39, 5] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 747 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113488 none CC1CCCC2=NC=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)N21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 167, 167, 167, 83, 83, 83, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 83, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 167, 83, 83, 83, 83, 14, 6, 6, 4, 4, 83, 83] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 516 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113488 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113488/1 /scratch/stefan/7770410/working/building/REAL300020113488 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 584) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/584 `/scratch/stefan/7770410/working/3D/584' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCC2=NC=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)N21) `REAL300020113488.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113488 none CC1CCCC2=NC=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)N21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 50, 70, 81, 81, 81, 81, 13, 13, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 13, 50, 50, 70, 70, 1, 1] 201 rigid atoms, others: [43, 41, 42, 11, 12, 13, 14, 15, 50, 51, 27, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 325 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113488 none CC1CCCC2=NC=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)N21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 88, 88, 88, 88, 88, 50, 50, 50, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 13, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 50, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13] 201 rigid atoms, others: [45, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 229 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113488 none CC1CCCC2=NC=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)N21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 88, 88, 88, 156, 201, 201, 201, 201, 201, 88, 88, 14, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 14, 14, 14, 14, 88, 156, 156, 201, 201, 14, 14] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 8, 9, 7, 34, 35, 36, 6, 28, 37, 39, 5] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 752 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113488 none CC1CCCC2=NC=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)N21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 167, 167, 167, 83, 83, 83, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 83, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 167, 83, 83, 83, 83, 15, 6, 6, 4, 4, 83, 83] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 516 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113488 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113488 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113488/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113488/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113488 Building REAL300020113489 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113489' /scratch/stefan/7770410/working/building/REAL300020113489 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113489 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113489/0 /scratch/stefan/7770410/working/building/REAL300020113489 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/585 `/scratch/stefan/7770410/working/3D/585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CN2CCCCC2=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113489.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113489 none O=C(CC1=CN2CCCCC2=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 5, 5, 5, 5, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 24, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 9, 9, 9, 32, 45, 47, 47, 47, 47, 9, 9, 1, 24, 24, 34, 34, 34, 34, 34, 34, 34, 34, 34, 6, 1, 1, 1, 1, 9, 32, 32, 45, 45, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 283 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113489 none O=C(CC1=CN2CCCCC2=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 5, 5, 5, 5, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 91, 104, 104, 104, 104, 104, 104, 104, 104, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 91, 91, 104, 104, 104, 104, 104, 104, 104, 104, 104, 30, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 380 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113489 none O=C(CC1=CN2CCCCC2=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 5, 5, 5, 5, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 34, 34, 34, 104, 104, 104, 180, 201, 201, 201, 201, 201, 104, 104, 34, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 34, 34, 34, 34, 104, 180, 180, 201, 201, 34, 34] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 36, 38, 37, 39, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 712 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113489 none O=C(CC1=CN2CCCCC2=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 5, 5, 5, 5, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 193, 201, 201, 201, 201, 201, 201, 201, 201, 49, 49, 49, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 49, 193, 193, 201, 201, 201, 201, 201, 201, 201, 201, 201, 101, 49, 49, 49, 49, 11, 6, 6, 4, 4, 49, 49] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 720 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113489 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113489/1 /scratch/stefan/7770410/working/building/REAL300020113489 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 586) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/586 `/scratch/stefan/7770410/working/3D/586' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CN2CCCCC2=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113489.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113489 none O=C(CC1=CN2CCCCC2=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 5, 5, 5, 5, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 24, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 9, 9, 9, 33, 47, 49, 49, 49, 49, 9, 9, 1, 24, 24, 33, 33, 33, 33, 33, 33, 33, 33, 33, 6, 1, 1, 1, 1, 9, 33, 33, 47, 47, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 290 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113489 none O=C(CC1=CN2CCCCC2=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 5, 5, 5, 5, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 90, 102, 102, 102, 102, 102, 102, 102, 102, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 90, 90, 102, 102, 102, 102, 102, 102, 102, 102, 102, 30, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 378 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113489 none O=C(CC1=CN2CCCCC2=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 5, 5, 5, 5, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 33, 33, 33, 102, 102, 102, 180, 201, 201, 201, 201, 201, 102, 102, 33, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 33, 33, 33, 33, 102, 180, 180, 201, 201, 33, 33] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 36, 38, 37, 39, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 712 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113489 none O=C(CC1=CN2CCCCC2=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 5, 5, 5, 5, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 193, 201, 201, 201, 201, 201, 201, 201, 201, 48, 48, 48, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 48, 193, 193, 201, 201, 201, 201, 201, 201, 201, 201, 201, 99, 48, 48, 48, 48, 10, 6, 6, 4, 4, 48, 48] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 728 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113489 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113489 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113489/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113489/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113489 Building REAL300020113490 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113490' /scratch/stefan/7770410/working/building/REAL300020113490 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113490 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113490/0 /scratch/stefan/7770410/working/building/REAL300020113490 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/587 `/scratch/stefan/7770410/working/3D/587' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)N1N=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1) `REAL300020113490.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113490 none CC(C)(C)N1N=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 15, 26, 26, 15, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 44, 63, 75, 75, 75, 75, 13, 13, 1, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 13, 44, 44, 63, 63, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 352 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113490 none CC(C)(C)N1N=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 76, 124, 124, 76, 76, 76, 59, 59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 76, 124, 124, 124, 124, 124, 124, 124, 124, 124, 59, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 466 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113490 none CC(C)(C)N1N=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 15, 15, 15, 76, 76, 76, 147, 187, 201, 201, 201, 201, 76, 76, 15, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 76, 147, 147, 187, 187, 15, 15] 201 rigid atoms, others: [1, 4, 5, 6, 7, 8, 27] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 726 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113490 none CC(C)(C)N1N=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 187, 187, 187, 76, 76, 76, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 76, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 187, 76, 76, 76, 76, 11, 6, 6, 4, 4, 76, 76] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 559 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113490 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113490/1 /scratch/stefan/7770410/working/building/REAL300020113490 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 588) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/588 `/scratch/stefan/7770410/working/3D/588' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)N1N=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1) `REAL300020113490.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113490 none CC(C)(C)N1N=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 15, 26, 26, 15, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 44, 63, 75, 75, 75, 75, 13, 13, 1, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 13, 44, 44, 63, 63, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 352 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113490 none CC(C)(C)N1N=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 76, 124, 124, 76, 76, 76, 59, 59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 76, 124, 124, 124, 124, 124, 124, 124, 124, 124, 59, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 466 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113490 none CC(C)(C)N1N=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 15, 15, 15, 76, 76, 76, 147, 187, 201, 201, 201, 201, 76, 76, 15, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 76, 147, 147, 187, 187, 15, 15] 201 rigid atoms, others: [1, 4, 5, 6, 7, 8, 27] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 726 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113490 none CC(C)(C)N1N=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 188, 188, 188, 76, 76, 76, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 76, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 188, 76, 76, 76, 76, 11, 6, 6, 4, 4, 76, 76] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 561 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113490 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113490 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113490/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113490/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113490 Building REAL300020113491 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113491' /scratch/stefan/7770410/working/building/REAL300020113491 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL300020113491 as failed and skipping /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `/scratch/stefan/7770410/failed' `/scratch/stefan/7770410/working/building/REAL300020113491' -> `/scratch/stefan/7770410/failed/REAL300020113491' Building REAL300020113492 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113492' /scratch/stefan/7770410/working/building/REAL300020113492 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113492 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113492/0 /scratch/stefan/7770410/working/building/REAL300020113492 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/589 `/scratch/stefan/7770410/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC2=NC=CC=C2C=C1) `REAL300020113492.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113492 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC2=NC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 13, 53, 80, 80, 80, 80, 80, 80, 80, 80, 80, 53, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13, 80, 80, 80, 80, 80] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 230 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113492 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC2=NC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 100, 100, 100, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 100, 200, 201, 201, 201, 201, 201, 201, 201, 201, 201, 200, 100, 100, 100, 100, 15, 6, 6, 4, 4, 100, 100, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 561 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113492 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC2=NC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 60, 81, 100, 100, 100, 100, 13, 13, 1, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 13, 60, 60, 81, 81, 1, 1, 13, 13, 13, 13, 13] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 379 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113492 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC2=NC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 13, 13, 13, 80, 80, 80, 165, 201, 201, 201, 201, 201, 80, 80, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 13, 13, 13, 13, 80, 165, 165, 201, 201, 13, 13, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 748 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113492 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113492/1 /scratch/stefan/7770410/working/building/REAL300020113492 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 590) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/590 `/scratch/stefan/7770410/working/3D/590' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC2=NC=CC=C2C=C1) `REAL300020113492.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113492 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC2=NC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 13, 53, 80, 80, 80, 80, 80, 80, 80, 80, 80, 53, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13, 80, 80, 80, 80, 80] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 229 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113492 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC2=NC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 100, 100, 100, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 100, 200, 201, 201, 201, 201, 201, 201, 201, 201, 201, 200, 100, 100, 100, 100, 15, 6, 6, 4, 4, 100, 100, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 561 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113492 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC2=NC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 61, 82, 99, 99, 99, 99, 13, 13, 1, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 13, 61, 61, 82, 82, 1, 1, 13, 13, 13, 13, 13] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 378 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113492 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC2=NC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 13, 13, 13, 80, 80, 80, 165, 201, 201, 201, 201, 201, 80, 80, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 13, 13, 13, 13, 80, 165, 165, 201, 201, 13, 13, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 742 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113492 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113492 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113492/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113492/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113492 Building REAL300020113493 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113493' /scratch/stefan/7770410/working/building/REAL300020113493 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113493 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113493/0 /scratch/stefan/7770410/working/building/REAL300020113493 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/591 `/scratch/stefan/7770410/working/3D/591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=C(F)C=C1F)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113493.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113493 none O=C(CC1=CC=C(F)C=C1F)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 15, 1, 1, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 25, 37, 37, 29, 37, 37, 37, 37, 1, 1, 1, 1, 1, 9, 9, 9, 31, 45, 49, 49, 49, 49, 9, 9, 1, 25, 25, 37, 37, 37, 6, 1, 1, 1, 1, 9, 31, 31, 45, 45, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 44, 11, 12, 13, 14, 15, 43, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 338 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113493 none O=C(CC1=CC=C(F)C=C1F)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 15, 1, 1, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 99, 114, 114, 104, 114, 114, 114, 114, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 99, 99, 114, 114, 114, 28, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [38, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 464 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113493 none O=C(CC1=CC=C(F)C=C1F)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 15, 1, 1, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 37, 37, 37, 114, 114, 114, 174, 201, 201, 201, 201, 201, 114, 114, 37, 5, 5, 1, 1, 1, 17, 37, 37, 37, 37, 114, 174, 174, 201, 201, 37, 37] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 690 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113493 none O=C(CC1=CC=C(F)C=C1F)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 15, 1, 1, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 198, 201, 201, 201, 201, 201, 201, 201, 51, 51, 51, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 51, 198, 198, 201, 201, 201, 101, 51, 51, 51, 51, 11, 6, 6, 4, 4, 51, 51] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 727 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113493 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113493/1 /scratch/stefan/7770410/working/building/REAL300020113493 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 592) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/592 `/scratch/stefan/7770410/working/3D/592' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=C(F)C=C1F)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113493.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113493 none O=C(CC1=CC=C(F)C=C1F)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 15, 1, 1, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 25, 37, 37, 29, 37, 37, 37, 37, 1, 1, 1, 1, 1, 10, 10, 10, 31, 45, 49, 49, 49, 49, 10, 10, 1, 25, 25, 37, 37, 37, 6, 1, 1, 1, 1, 10, 31, 31, 45, 45, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 44, 11, 12, 13, 14, 15, 43, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 333 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113493 none O=C(CC1=CC=C(F)C=C1F)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 15, 1, 1, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 98, 114, 114, 103, 114, 114, 114, 114, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 10, 98, 98, 114, 114, 114, 29, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10] 201 rigid atoms, others: [38, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 464 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113493 none O=C(CC1=CC=C(F)C=C1F)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 15, 1, 1, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 37, 37, 37, 114, 114, 114, 174, 201, 201, 201, 201, 201, 114, 114, 37, 5, 5, 1, 1, 1, 17, 37, 37, 37, 37, 114, 174, 174, 201, 201, 37, 37] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 690 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113493 none O=C(CC1=CC=C(F)C=C1F)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 15, 1, 1, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 198, 201, 201, 201, 201, 201, 201, 201, 51, 51, 51, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 51, 198, 198, 201, 201, 201, 99, 51, 51, 51, 51, 11, 6, 6, 4, 4, 51, 51] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 724 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113493 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113493 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113493/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113493/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113493 Building REAL300020113494 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113494' /scratch/stefan/7770410/working/building/REAL300020113494 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113494 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113494/0 /scratch/stefan/7770410/working/building/REAL300020113494 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 593) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/593 `/scratch/stefan/7770410/working/3D/593' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(F)C=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113494.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113494 none CC1=C(F)C=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 29, 43, 44, 44, 44, 44, 11, 11, 1, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 11, 29, 29, 43, 43, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 44, 10, 11, 12, 13, 14, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 208 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113494 none CC1=C(F)C=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 97, 97, 97, 97, 97, 29, 29, 29, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 10, 10, 10, 10, 1, 1, 11, 97, 97, 97, 97, 97, 97, 29, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11] 201 rigid atoms, others: [38, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 198 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113494 none CC1=C(F)C=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 24, 24, 24, 97, 97, 97, 156, 201, 201, 201, 201, 201, 97, 97, 24, 2, 2, 2, 1, 1, 1, 9, 24, 24, 24, 24, 97, 156, 156, 201, 201, 24, 24] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 742 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113494 none CC1=C(F)C=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 79, 79, 79, 45, 45, 45, 11, 11, 11, 5, 3, 1, 1, 1, 1, 1, 1, 11, 11, 45, 201, 201, 201, 201, 201, 201, 79, 45, 45, 45, 45, 11, 5, 5, 3, 3, 45, 45] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 400 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113494 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113494/1 /scratch/stefan/7770410/working/building/REAL300020113494 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 594) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/594 `/scratch/stefan/7770410/working/3D/594' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(F)C=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113494.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113494 none CC1=C(F)C=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 29, 43, 44, 44, 44, 44, 11, 11, 1, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 11, 29, 29, 43, 43, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 44, 10, 11, 12, 13, 14, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 208 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113494 none CC1=C(F)C=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 97, 97, 97, 97, 97, 29, 29, 29, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 10, 10, 10, 10, 1, 1, 11, 97, 97, 97, 97, 97, 97, 29, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11] 201 rigid atoms, others: [38, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 198 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113494 none CC1=C(F)C=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 24, 24, 24, 97, 97, 97, 156, 201, 201, 201, 201, 201, 97, 97, 24, 2, 2, 2, 1, 1, 1, 9, 24, 24, 24, 24, 97, 156, 156, 201, 201, 24, 24] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 742 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113494 none CC1=C(F)C=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 79, 79, 79, 45, 45, 45, 11, 11, 11, 5, 3, 1, 1, 1, 1, 1, 1, 11, 11, 45, 201, 201, 201, 201, 201, 201, 79, 45, 45, 45, 45, 11, 5, 5, 3, 3, 45, 45] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 402 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113494 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113494 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113494/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113494/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113494 Building REAL300020113495 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113495' /scratch/stefan/7770410/working/building/REAL300020113495 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113495 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113495/0 /scratch/stefan/7770410/working/building/REAL300020113495 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/595 `/scratch/stefan/7770410/working/3D/595' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(C)C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1C) `REAL300020113495.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113495 none COC1=C(C)C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 6, 6, 12, 12, 12, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 35, 50, 58, 58, 58, 58, 11, 11, 1, 12, 12, 12, 20, 20, 20, 12, 12, 12, 12, 6, 1, 1, 1, 1, 11, 35, 35, 50, 50, 1, 1, 12, 12, 12, 12] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 272 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113495 none COC1=C(C)C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 36, 36, 67, 67, 67, 36, 36, 36, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 67, 67, 67, 105, 105, 105, 67, 67, 67, 67, 36, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 67, 67, 67, 67] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 377 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113495 none COC1=C(C)C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 67, 67, 67, 152, 191, 201, 201, 201, 201, 67, 67, 12, 1, 1, 1, 3, 3, 3, 2, 2, 2, 1, 4, 12, 12, 12, 12, 67, 152, 152, 191, 191, 12, 12, 1, 2, 2, 2] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 48, 35, 26, 27, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51]) total number of confs: 755 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113495 none COC1=C(C)C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 121, 121, 201, 201, 201, 121, 121, 121, 59, 59, 59, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 59, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 121, 59, 59, 59, 59, 14, 6, 6, 4, 4, 59, 59, 201, 201, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 894 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113495 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113495/1 /scratch/stefan/7770410/working/building/REAL300020113495 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 596) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/596 `/scratch/stefan/7770410/working/3D/596' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(C)C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1C) `REAL300020113495.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113495 none COC1=C(C)C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 6, 6, 11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 35, 50, 58, 58, 58, 58, 11, 11, 1, 11, 11, 11, 19, 19, 19, 11, 11, 11, 11, 6, 1, 1, 1, 1, 11, 35, 35, 50, 50, 1, 1, 11, 11, 11, 11] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 269 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113495 none COC1=C(C)C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 36, 36, 66, 66, 66, 36, 36, 36, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 66, 66, 66, 104, 104, 104, 66, 66, 66, 66, 36, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 66, 66, 66, 66] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 374 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113495 none COC1=C(C)C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 66, 66, 66, 151, 191, 201, 201, 201, 201, 66, 66, 11, 1, 1, 1, 3, 3, 3, 2, 2, 2, 1, 3, 11, 11, 11, 11, 66, 151, 151, 191, 191, 11, 11, 1, 2, 2, 2] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 48, 35, 26, 27, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51]) total number of confs: 759 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113495 none COC1=C(C)C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 122, 122, 201, 201, 201, 122, 122, 122, 60, 60, 60, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 60, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 122, 60, 60, 60, 60, 15, 6, 6, 4, 4, 60, 60, 201, 201, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 888 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113495 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113495 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113495/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113495/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113495 Building REAL300020113496 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113496' /scratch/stefan/7770410/working/building/REAL300020113496 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113496 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113496/0 /scratch/stefan/7770410/working/building/REAL300020113496 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/597 `/scratch/stefan/7770410/working/3D/597' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1) `REAL300020113496.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113496 none CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 34, 50, 64, 64, 64, 64, 11, 11, 1, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 34, 34, 50, 50, 1, 1, 22, 22, 22, 22] 201 rigid atoms, others: [4, 5, 6, 7, 8, 20, 36, 27, 28, 29, 30, 37] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 286 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113496 none CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 39, 39, 39, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 12, 12, 12, 12, 1, 1, 11, 97, 97, 97, 97, 97, 39, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 97, 97, 97, 97] 201 rigid atoms, others: [7, 8, 9, 10, 11, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 311 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113496 none CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 6, 6, 6, 22, 22, 22, 97, 97, 97, 182, 200, 201, 201, 201, 201, 97, 97, 22, 1, 1, 2, 2, 2, 6, 22, 22, 22, 22, 97, 182, 182, 200, 200, 22, 22, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 38, 39, 40, 41, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 648 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113496 none CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 126, 126, 126, 64, 64, 64, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 64, 201, 201, 201, 201, 201, 126, 64, 64, 64, 64, 12, 6, 6, 4, 4, 64, 64, 201, 201, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 661 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113496 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113496/1 /scratch/stefan/7770410/working/building/REAL300020113496 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 598) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/598 `/scratch/stefan/7770410/working/3D/598' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1) `REAL300020113496.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113496 none CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 34, 50, 64, 64, 64, 64, 11, 11, 1, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 34, 34, 50, 50, 1, 1, 22, 22, 22, 22] 201 rigid atoms, others: [4, 5, 6, 7, 8, 20, 36, 27, 28, 29, 30, 37] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 286 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113496 none CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 39, 39, 39, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 12, 12, 12, 12, 1, 1, 11, 97, 97, 97, 97, 97, 39, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 97, 97, 97, 97] 201 rigid atoms, others: [7, 8, 9, 10, 11, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 311 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113496 none CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 6, 6, 6, 22, 22, 22, 97, 97, 97, 182, 200, 201, 201, 201, 201, 97, 97, 22, 1, 1, 2, 2, 2, 6, 22, 22, 22, 22, 97, 182, 182, 200, 200, 22, 22, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 38, 39, 40, 41, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 648 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113496 none CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 126, 126, 126, 64, 64, 64, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 64, 201, 201, 201, 201, 201, 126, 64, 64, 64, 64, 12, 6, 6, 4, 4, 64, 64, 201, 201, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 661 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113496 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113496 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113496/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113496/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113496 Building REAL300020113497 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113497' /scratch/stefan/7770410/working/building/REAL300020113497 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113497 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113497/0 /scratch/stefan/7770410/working/building/REAL300020113497 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/599 `/scratch/stefan/7770410/working/3D/599' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1F) `REAL300020113497.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113497 none CC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 8, 18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 56, 74, 92, 92, 92, 92, 12, 12, 1, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 12, 56, 56, 74, 74, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 379 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113497 none CC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 52, 104, 104, 45, 45, 45, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 17, 17, 17, 17, 1, 1, 12, 104, 104, 104, 104, 104, 104, 104, 104, 45, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 432 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113497 none CC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 18, 18, 18, 104, 104, 104, 174, 201, 201, 201, 201, 201, 104, 104, 18, 1, 1, 2, 2, 2, 1, 1, 1, 8, 18, 18, 18, 18, 104, 174, 174, 201, 201, 18, 18] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 25, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 678 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113497 none CC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 168, 168, 168, 94, 94, 94, 20, 20, 20, 6, 4, 1, 1, 1, 1, 1, 1, 20, 20, 94, 201, 201, 201, 201, 201, 201, 201, 201, 168, 94, 94, 94, 94, 20, 6, 6, 4, 4, 94, 94] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 526 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113497 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113497/1 /scratch/stefan/7770410/working/building/REAL300020113497 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 600) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/600 `/scratch/stefan/7770410/working/3D/600' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1F) `REAL300020113497.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113497 none CC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 8, 18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 54, 72, 92, 92, 92, 92, 12, 12, 1, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 12, 54, 54, 72, 72, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 377 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113497 none CC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 51, 103, 103, 45, 45, 45, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 17, 17, 17, 17, 1, 1, 12, 103, 103, 103, 103, 103, 103, 103, 103, 45, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 428 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113497 none CC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 18, 18, 18, 103, 103, 103, 174, 201, 201, 201, 201, 201, 103, 103, 18, 1, 1, 2, 2, 2, 1, 1, 1, 8, 18, 18, 18, 18, 103, 174, 174, 201, 201, 18, 18] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 25, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 686 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113497 none CC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 167, 167, 167, 92, 92, 92, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 92, 201, 201, 201, 201, 201, 201, 201, 201, 167, 92, 92, 92, 92, 18, 6, 6, 4, 4, 92, 92] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 530 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113497 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113497 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113497/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113497/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113497 Building REAL300020113498 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113498' /scratch/stefan/7770410/working/building/REAL300020113498 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113498 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113498/0 /scratch/stefan/7770410/working/building/REAL300020113498 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 601) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/601 `/scratch/stefan/7770410/working/3D/601' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)NC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113498.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113498 none CCS(=O)(=O)NC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 118, 118, 118, 118, 104, 35, 104, 35, 35, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 119, 119, 119, 119, 119, 118, 104, 104, 104, 104, 35, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 451 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113498 none CCS(=O)(=O)NC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 200, 116, 200, 116, 116, 48, 48, 48, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 48, 201, 201, 201, 201, 201, 201, 200, 200, 200, 200, 116, 48, 48, 48, 48, 10, 6, 6, 4, 4, 48, 48] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 739 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113498 none CCS(=O)(=O)NC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 32, 32, 32, 32, 27, 6, 27, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 31, 43, 45, 45, 45, 45, 9, 9, 1, 35, 35, 35, 35, 35, 32, 27, 27, 27, 27, 6, 1, 1, 1, 1, 9, 31, 31, 43, 43, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113498 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113498/1 /scratch/stefan/7770410/working/building/REAL300020113498 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 602) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/602 `/scratch/stefan/7770410/working/3D/602' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)NC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113498.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113498 none CCS(=O)(=O)NC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 118, 118, 118, 118, 104, 35, 104, 35, 35, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 119, 119, 119, 119, 119, 118, 104, 104, 104, 104, 35, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 451 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113498 none CCS(=O)(=O)NC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 200, 116, 200, 116, 116, 48, 48, 48, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 48, 201, 201, 201, 201, 201, 201, 200, 200, 200, 200, 116, 48, 48, 48, 48, 10, 6, 6, 4, 4, 48, 48] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 739 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113498 none CCS(=O)(=O)NC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 32, 32, 32, 32, 27, 6, 27, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 31, 43, 45, 45, 45, 45, 9, 9, 1, 35, 35, 35, 35, 35, 32, 27, 27, 27, 27, 6, 1, 1, 1, 1, 9, 31, 31, 43, 43, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113498 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113498 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113498/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113498/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113498 Building REAL300020113499 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113499' /scratch/stefan/7770410/working/building/REAL300020113499 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113499 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113499/0 /scratch/stefan/7770410/working/building/REAL300020113499 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 603) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/603 `/scratch/stefan/7770410/working/3D/603' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Cl)C=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113499.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113499 none CC1=C(Cl)C=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 23, 14, 23, 23, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 30, 44, 45, 45, 45, 45, 11, 11, 1, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 11, 30, 30, 44, 44, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 44, 10, 11, 12, 13, 14, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 249 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113499 none CC1=C(Cl)C=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 96, 71, 96, 96, 29, 29, 29, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 10, 10, 10, 10, 1, 1, 11, 96, 96, 96, 96, 96, 96, 29, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11] 201 rigid atoms, others: [38, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 290 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113499 none CC1=C(Cl)C=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 23, 23, 23, 96, 96, 96, 154, 201, 201, 201, 201, 201, 96, 96, 23, 2, 2, 2, 1, 1, 1, 9, 23, 23, 23, 23, 96, 154, 154, 201, 201, 23, 23] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 750 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113499 none CC1=C(Cl)C=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 80, 80, 80, 45, 45, 45, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 45, 201, 201, 201, 201, 201, 201, 80, 45, 45, 45, 45, 10, 5, 5, 3, 3, 45, 45] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 401 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113499 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113499/1 /scratch/stefan/7770410/working/building/REAL300020113499 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 604) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/604 `/scratch/stefan/7770410/working/3D/604' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Cl)C=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113499.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113499 none CC1=C(Cl)C=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 23, 14, 23, 23, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 30, 44, 45, 45, 45, 45, 11, 11, 1, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 11, 30, 30, 44, 44, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 44, 10, 11, 12, 13, 14, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 249 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113499 none CC1=C(Cl)C=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 96, 71, 96, 96, 29, 29, 29, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 10, 10, 10, 10, 1, 1, 11, 96, 96, 96, 96, 96, 96, 29, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11] 201 rigid atoms, others: [38, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 290 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113499 none CC1=C(Cl)C=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 23, 23, 23, 96, 96, 96, 154, 201, 201, 201, 201, 201, 96, 96, 23, 2, 2, 2, 1, 1, 1, 9, 23, 23, 23, 23, 96, 154, 154, 201, 201, 23, 23] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 750 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113499 none CC1=C(Cl)C=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 80, 80, 80, 45, 45, 45, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 45, 201, 201, 201, 201, 201, 201, 80, 45, 45, 45, 45, 10, 5, 5, 3, 3, 45, 45] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 403 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113499 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113499 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113499/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113499/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113499 Building REAL300020113500 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113500' /scratch/stefan/7770410/working/building/REAL300020113500 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113500 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113500/0 /scratch/stefan/7770410/working/building/REAL300020113500 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 605) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/605 `/scratch/stefan/7770410/working/3D/605' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(Cl)C=CS1) `REAL300020113500.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113500 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(Cl)C=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 16, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 7, 7, 7, 1, 1, 1, 1, 1, 9, 15, 21, 21, 21, 21, 1, 1, 7, 24, 71, 71, 71, 71, 71, 24, 7, 7, 7, 7, 1, 9, 9, 15, 15, 7, 7, 71, 71] 184 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 200 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113500 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(Cl)C=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 16, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 73, 73, 73, 25, 25, 25, 8, 4, 1, 1, 1, 1, 1, 1, 25, 25, 73, 115, 184, 184, 184, 184, 184, 115, 73, 73, 73, 73, 25, 8, 8, 4, 4, 73, 73, 184, 184] 184 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 444 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113500 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(Cl)C=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 16, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 36, 52, 70, 70, 70, 70, 7, 7, 1, 6, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 7, 36, 36, 52, 52, 1, 1, 23, 23] 184 rigid atoms, others: [2, 3, 4, 5, 6, 18, 35, 36, 26, 27, 28, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113500 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(Cl)C=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 16, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 23, 23, 23, 71, 71, 71, 155, 184, 184, 184, 184, 184, 71, 71, 23, 1, 1, 1, 1, 1, 1, 7, 23, 23, 23, 23, 71, 155, 155, 184, 184, 23, 23, 1, 1] 184 rigid atoms, others: [1, 37, 38, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 689 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113500 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113500/1 /scratch/stefan/7770410/working/building/REAL300020113500 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 606) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/606 `/scratch/stefan/7770410/working/3D/606' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(Cl)C=CS1) `REAL300020113500.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113500/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113500 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(Cl)C=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 16, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 7, 7, 7, 1, 1, 1, 1, 1, 9, 15, 21, 21, 21, 21, 1, 1, 7, 24, 71, 71, 71, 71, 71, 24, 7, 7, 7, 7, 1, 9, 9, 15, 15, 7, 7, 71, 71] 184 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 200 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113500 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(Cl)C=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 16, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 73, 73, 73, 25, 25, 25, 8, 4, 1, 1, 1, 1, 1, 1, 25, 25, 73, 116, 185, 185, 185, 185, 185, 116, 73, 73, 73, 73, 25, 8, 8, 4, 4, 73, 73, 185, 185] 185 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 448 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113500 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(Cl)C=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 16, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 36, 52, 70, 70, 70, 70, 7, 7, 1, 6, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 7, 36, 36, 52, 52, 1, 1, 23, 23] 184 rigid atoms, others: [2, 3, 4, 5, 6, 18, 35, 36, 26, 27, 28, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113500 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(Cl)C=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 16, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 23, 23, 23, 71, 71, 71, 155, 184, 184, 184, 184, 184, 71, 71, 23, 1, 1, 1, 1, 1, 1, 7, 23, 23, 23, 23, 71, 155, 155, 184, 184, 23, 23, 1, 1] 184 rigid atoms, others: [1, 37, 38, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 689 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113500 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113500 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113500/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113500/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113500 Building REAL300020113501 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113501' /scratch/stefan/7770410/working/building/REAL300020113501 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113501 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113501/0 /scratch/stefan/7770410/working/building/REAL300020113501 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/607 `/scratch/stefan/7770410/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)C1=CC=NC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113501.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113501 none O=C(CNC(=O)C1=CC=NC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 29, 35, 35, 35, 55, 55, 35, 55, 55, 1, 1, 1, 1, 1, 8, 8, 8, 22, 34, 34, 34, 34, 34, 8, 8, 1, 29, 29, 35, 55, 55, 55, 55, 5, 1, 1, 1, 1, 8, 22, 22, 34, 34, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 46, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 359 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113501 none O=C(CNC(=O)C1=CC=NC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 94, 105, 105, 105, 127, 127, 105, 127, 127, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 94, 94, 105, 127, 127, 127, 127, 22, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 502 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113501 none O=C(CNC(=O)C1=CC=NC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 11, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 29, 29, 55, 55, 55, 127, 127, 127, 177, 201, 201, 201, 201, 201, 127, 127, 55, 11, 11, 3, 1, 1, 1, 1, 29, 55, 55, 55, 55, 127, 177, 177, 201, 201, 55, 55] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 693 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113501 none O=C(CNC(=O)C1=CC=NC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 199, 201, 201, 201, 201, 201, 201, 201, 201, 34, 34, 34, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 34, 199, 199, 201, 201, 201, 201, 201, 63, 34, 34, 34, 34, 7, 4, 4, 2, 2, 34, 34] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 717 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113501 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113501/1 /scratch/stefan/7770410/working/building/REAL300020113501 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 608) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/608 `/scratch/stefan/7770410/working/3D/608' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)C1=CC=NC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113501.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113501 none O=C(CNC(=O)C1=CC=NC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 29, 35, 35, 35, 54, 54, 35, 54, 54, 1, 1, 1, 1, 1, 8, 8, 8, 22, 34, 34, 34, 34, 34, 8, 8, 1, 29, 29, 35, 54, 54, 54, 54, 5, 1, 1, 1, 1, 8, 22, 22, 34, 34, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 46, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 354 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113501 none O=C(CNC(=O)C1=CC=NC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 92, 103, 103, 103, 125, 125, 103, 125, 125, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 92, 92, 103, 125, 125, 125, 125, 22, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 496 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113501 none O=C(CNC(=O)C1=CC=NC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 11, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 28, 28, 54, 54, 54, 125, 125, 125, 177, 201, 201, 201, 201, 201, 125, 125, 54, 11, 11, 3, 1, 1, 1, 1, 28, 54, 54, 54, 54, 125, 177, 177, 201, 201, 54, 54] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 701 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113501 none O=C(CNC(=O)C1=CC=NC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 199, 201, 201, 201, 201, 201, 201, 201, 201, 34, 34, 34, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 34, 199, 199, 201, 201, 201, 201, 201, 63, 34, 34, 34, 34, 7, 4, 4, 2, 2, 34, 34] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 719 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113501 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113501 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113501/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113501/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113501 Building REAL300020113502 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113502' /scratch/stefan/7770410/working/building/REAL300020113502 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113502 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113502/0 /scratch/stefan/7770410/working/building/REAL300020113502 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/609 `/scratch/stefan/7770410/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1CCC2=CC=CC=C21)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113502.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113502 none O=C(CN1CCC2=CC=CC=C21)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 16, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 9, 9, 9, 29, 44, 49, 49, 49, 49, 9, 9, 1, 16, 16, 24, 24, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 9, 29, 29, 44, 44, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 16, 49, 50, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 264 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113502 none O=C(CN1CCC2=CC=CC=C21)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 72, 97, 97, 97, 97, 97, 97, 97, 97, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 72, 72, 97, 97, 97, 97, 97, 97, 97, 97, 32, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9] 201 rigid atoms, others: [44, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 345 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113502 none O=C(CN1CCC2=CC=CC=C21)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 24, 24, 24, 97, 97, 97, 173, 201, 201, 201, 201, 201, 97, 97, 24, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 24, 24, 24, 24, 97, 173, 173, 201, 201, 24, 24] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 36, 38, 37, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 732 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113502 none O=C(CN1CCC2=CC=CC=C21)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 173, 201, 201, 201, 201, 201, 201, 201, 201, 50, 50, 50, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 50, 173, 173, 201, 201, 201, 201, 201, 201, 201, 201, 101, 50, 50, 50, 50, 12, 6, 6, 4, 4, 50, 50] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 684 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113502 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113502/1 /scratch/stefan/7770410/working/building/REAL300020113502 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 610) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/610 `/scratch/stefan/7770410/working/3D/610' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1CCC2=CC=CC=C21)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113502.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113502 none O=C(CN1CCC2=CC=CC=C21)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 16, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 9, 9, 9, 29, 44, 49, 49, 49, 49, 9, 9, 1, 16, 16, 24, 24, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 9, 29, 29, 44, 44, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 16, 49, 50, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 264 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113502 none O=C(CN1CCC2=CC=CC=C21)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 71, 96, 96, 96, 96, 96, 96, 96, 96, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 71, 71, 96, 96, 96, 96, 96, 96, 96, 96, 32, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9] 201 rigid atoms, others: [44, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 342 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113502 none O=C(CN1CCC2=CC=CC=C21)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 24, 24, 24, 96, 96, 96, 172, 201, 201, 201, 201, 201, 96, 96, 24, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 24, 24, 24, 24, 96, 172, 172, 201, 201, 24, 24] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 36, 38, 37, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 737 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113502 none O=C(CN1CCC2=CC=CC=C21)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 172, 201, 201, 201, 201, 201, 201, 201, 201, 49, 49, 49, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 49, 172, 172, 201, 201, 201, 201, 201, 201, 201, 201, 102, 49, 49, 49, 49, 11, 6, 6, 4, 4, 49, 49] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 682 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113502 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113502 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113502/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113502/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113502 Building REAL300020113503 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113503' /scratch/stefan/7770410/working/building/REAL300020113503 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113503 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113503/0 /scratch/stefan/7770410/working/building/REAL300020113503 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/611 `/scratch/stefan/7770410/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCOCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113503.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113503 none O=C(CCOCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 17, 17, 25, 49, 66, 66, 60, 66, 66, 1, 1, 1, 1, 1, 8, 8, 8, 25, 37, 39, 39, 39, 39, 8, 8, 1, 17, 17, 17, 17, 49, 49, 66, 66, 66, 66, 66, 5, 1, 1, 1, 1, 8, 25, 25, 37, 37, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 411 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113503 none O=C(CCOCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 49, 49, 64, 111, 127, 127, 122, 127, 127, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 49, 49, 49, 49, 111, 111, 127, 127, 127, 127, 127, 20, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 550 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113503 none O=C(CCOCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 29, 21, 11, 3, 1, 1, 1, 1, 1, 1, 1, 35, 36, 66, 66, 66, 127, 127, 127, 183, 201, 201, 201, 201, 201, 127, 127, 66, 29, 29, 21, 21, 3, 3, 1, 1, 1, 1, 1, 36, 66, 66, 66, 66, 127, 183, 183, 201, 201, 66, 66] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 39, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 744 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113503 none O=C(CCOCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 150, 150, 177, 201, 201, 201, 201, 201, 201, 39, 39, 39, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 39, 150, 150, 150, 150, 201, 201, 201, 201, 201, 201, 201, 78, 39, 39, 39, 39, 9, 5, 5, 3, 3, 39, 39] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 758 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113503 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113503/1 /scratch/stefan/7770410/working/building/REAL300020113503 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 612) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/612 `/scratch/stefan/7770410/working/3D/612' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCOCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113503.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113503 none O=C(CCOCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 17, 17, 25, 49, 66, 66, 60, 66, 66, 1, 1, 1, 1, 1, 8, 8, 8, 25, 37, 39, 39, 39, 39, 8, 8, 1, 17, 17, 17, 17, 49, 49, 66, 66, 66, 66, 66, 5, 1, 1, 1, 1, 8, 25, 25, 37, 37, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 411 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113503 none O=C(CCOCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 49, 49, 64, 111, 127, 127, 122, 127, 127, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 49, 49, 49, 49, 111, 111, 127, 127, 127, 127, 127, 20, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 550 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113503 none O=C(CCOCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 29, 21, 11, 3, 1, 1, 1, 1, 1, 1, 1, 35, 36, 66, 66, 66, 127, 127, 127, 183, 201, 201, 201, 201, 201, 127, 127, 66, 29, 29, 21, 21, 3, 3, 1, 1, 1, 1, 1, 36, 66, 66, 66, 66, 127, 183, 183, 201, 201, 66, 66] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 39, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 744 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113503 none O=C(CCOCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 150, 150, 177, 201, 201, 201, 201, 201, 201, 39, 39, 39, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 39, 150, 150, 150, 150, 201, 201, 201, 201, 201, 201, 201, 78, 39, 39, 39, 39, 9, 5, 5, 3, 3, 39, 39] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 758 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113503 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113503 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113503/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113503/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113503 Building REAL300020113504 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113504' /scratch/stefan/7770410/working/building/REAL300020113504 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113504 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113504/0 /scratch/stefan/7770410/working/building/REAL300020113504 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/613 `/scratch/stefan/7770410/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCN1C=CC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113504.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113504 none O=C(CCCN1C=CC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 20, 13, 30, 46, 46, 46, 46, 1, 1, 1, 1, 1, 7, 7, 7, 19, 31, 32, 32, 32, 32, 7, 7, 1, 20, 20, 22, 22, 26, 25, 46, 46, 46, 5, 1, 1, 1, 1, 7, 19, 19, 31, 31, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 315 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113504 none O=C(CCCN1C=CC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 83, 52, 107, 132, 132, 132, 132, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 7, 83, 83, 85, 85, 95, 95, 132, 132, 132, 17, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 642 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113504 none O=C(CCCN1C=CC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 13, 9, 5, 1, 1, 1, 1, 1, 1, 29, 29, 46, 46, 46, 132, 132, 132, 175, 201, 201, 201, 201, 201, 132, 132, 46, 13, 13, 9, 9, 5, 5, 1, 1, 1, 29, 46, 46, 46, 46, 132, 175, 175, 201, 201, 46, 46] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 692 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113504 none O=C(CCCN1C=CC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 148, 103, 172, 201, 201, 201, 201, 34, 34, 34, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 34, 148, 148, 148, 148, 156, 157, 201, 201, 201, 48, 34, 34, 34, 34, 9, 5, 5, 3, 3, 34, 34] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 939 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113504 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113504/1 /scratch/stefan/7770410/working/building/REAL300020113504 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 614) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/614 `/scratch/stefan/7770410/working/3D/614' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCN1C=CC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113504.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113504/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113504 none O=C(CCCN1C=CC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 20, 12, 29, 46, 46, 46, 46, 1, 1, 1, 1, 1, 7, 7, 7, 19, 31, 32, 32, 32, 32, 7, 7, 1, 20, 20, 21, 21, 25, 24, 46, 46, 46, 5, 1, 1, 1, 1, 7, 19, 19, 31, 31, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 311 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113504 none O=C(CCCN1C=CC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 83, 51, 106, 132, 132, 132, 132, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 7, 83, 83, 84, 84, 94, 94, 132, 132, 132, 17, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 639 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113504 none O=C(CCCN1C=CC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 13, 9, 5, 1, 1, 1, 1, 1, 1, 29, 29, 46, 46, 46, 132, 132, 132, 176, 201, 201, 201, 201, 201, 132, 132, 46, 13, 13, 9, 9, 5, 5, 1, 1, 1, 29, 46, 46, 46, 46, 132, 176, 176, 201, 201, 46, 46] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 692 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113504 none O=C(CCCN1C=CC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 148, 103, 172, 201, 201, 201, 201, 34, 34, 34, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 34, 148, 148, 148, 148, 156, 157, 201, 201, 201, 48, 34, 34, 34, 34, 9, 5, 5, 3, 3, 34, 34] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 939 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113504 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113504 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113504/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113504/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113504 Building REAL300020113505 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113505' /scratch/stefan/7770410/working/building/REAL300020113505 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113505 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113505/0 /scratch/stefan/7770410/working/building/REAL300020113505 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 615) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/615 `/scratch/stefan/7770410/working/3D/615' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)CC(=O)NCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113505.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113505 none CC(C)(C)CC(=O)NCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 116, 118, 83, 83, 83, 81, 21, 21, 21, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 83, 81, 81, 21, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [14, 47, 16, 17, 18, 25, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 539 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113505 none CC(C)(C)CC(=O)NCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 200, 201, 149, 149, 149, 147, 58, 58, 58, 33, 33, 33, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 33, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 149, 147, 147, 58, 33, 33, 33, 33, 8, 4, 4, 2, 2, 33, 33] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 866 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113505 none CC(C)(C)CC(=O)NCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 40, 26, 26, 26, 22, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 20, 32, 32, 32, 32, 32, 7, 7, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 26, 22, 22, 5, 1, 1, 1, 1, 7, 20, 20, 32, 32, 1, 1] 201 rigid atoms, others: [11, 15, 44, 43, 12, 13, 14, 45, 52, 46, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 310 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113505 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113505/1 /scratch/stefan/7770410/working/building/REAL300020113505 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 616) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/616 `/scratch/stefan/7770410/working/3D/616' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)CC(=O)NCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113505.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113505/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113505 none CC(C)(C)CC(=O)NCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 115, 118, 83, 83, 83, 81, 21, 21, 21, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 83, 81, 81, 21, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [14, 47, 16, 17, 18, 25, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 546 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113505 none CC(C)(C)CC(=O)NCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 200, 201, 149, 149, 149, 147, 57, 57, 57, 32, 32, 32, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 32, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 149, 147, 147, 57, 32, 32, 32, 32, 7, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 867 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113505 none CC(C)(C)CC(=O)NCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 25, 25, 25, 22, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 20, 32, 32, 32, 32, 32, 7, 7, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 25, 22, 22, 5, 1, 1, 1, 1, 7, 20, 20, 32, 32, 1, 1] 201 rigid atoms, others: [11, 15, 44, 43, 12, 13, 14, 45, 52, 46, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 306 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113505 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113505 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113505/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113505/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113505 Building REAL300020113506 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113506' /scratch/stefan/7770410/working/building/REAL300020113506 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113506 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113506/0 /scratch/stefan/7770410/working/building/REAL300020113506 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 617) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/617 `/scratch/stefan/7770410/working/3D/617' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1C=CC2=CC=CC=C21)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113506.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113506 none O=C(CN1C=CC2=CC=CC=C21)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 20, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 8, 8, 8, 23, 34, 34, 34, 34, 34, 8, 8, 1, 20, 20, 38, 38, 38, 38, 38, 38, 5, 1, 1, 1, 1, 8, 23, 23, 34, 34, 1, 1] 201 rigid atoms, others: [48, 38, 39, 40, 41, 12, 13, 14, 15, 16, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 237 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113506 none O=C(CN1C=CC2=CC=CC=C21)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 71, 117, 117, 117, 117, 117, 117, 117, 117, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 71, 71, 117, 117, 117, 117, 117, 117, 19, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 362 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113506 none O=C(CN1C=CC2=CC=CC=C21)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 38, 38, 38, 117, 117, 117, 172, 201, 201, 201, 201, 201, 117, 117, 38, 7, 7, 1, 1, 1, 1, 1, 1, 23, 38, 38, 38, 38, 117, 172, 172, 201, 201, 38, 38] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 36, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 692 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113506 none O=C(CN1C=CC2=CC=CC=C21)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 145, 201, 201, 201, 201, 201, 201, 201, 201, 36, 36, 36, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 36, 145, 145, 201, 201, 201, 201, 201, 201, 54, 36, 36, 36, 36, 9, 4, 4, 2, 2, 36, 36] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 641 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113506 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113506/1 /scratch/stefan/7770410/working/building/REAL300020113506 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 618) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/618 `/scratch/stefan/7770410/working/3D/618' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1C=CC2=CC=CC=C21)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113506.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113506/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113506 none O=C(CN1C=CC2=CC=CC=C21)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 20, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 8, 8, 8, 23, 34, 34, 34, 34, 34, 8, 8, 1, 20, 20, 38, 38, 38, 38, 38, 38, 5, 1, 1, 1, 1, 8, 23, 23, 34, 34, 1, 1] 201 rigid atoms, others: [48, 38, 39, 40, 41, 12, 13, 14, 15, 16, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 237 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113506 none O=C(CN1C=CC2=CC=CC=C21)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 71, 117, 117, 117, 117, 117, 117, 117, 117, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 71, 71, 117, 117, 117, 117, 117, 117, 19, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 362 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113506 none O=C(CN1C=CC2=CC=CC=C21)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 38, 38, 38, 117, 117, 117, 171, 201, 201, 201, 201, 201, 117, 117, 38, 7, 7, 1, 1, 1, 1, 1, 1, 23, 38, 38, 38, 38, 117, 171, 171, 201, 201, 38, 38] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 36, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 692 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113506 none O=C(CN1C=CC2=CC=CC=C21)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 146, 201, 201, 201, 201, 201, 201, 201, 201, 36, 36, 36, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 36, 146, 146, 201, 201, 201, 201, 201, 201, 54, 36, 36, 36, 36, 9, 4, 4, 2, 2, 36, 36] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 642 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113506 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113506 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113506/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113506/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113506 Building REAL300020113507 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113507' /scratch/stefan/7770410/working/building/REAL300020113507 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113507 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113507/0 /scratch/stefan/7770410/working/building/REAL300020113507 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 619) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/619 `/scratch/stefan/7770410/working/3D/619' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=NC=CS1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113507.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113507 none O=C(CCC1=NC=CS1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 1, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 29, 36, 66, 66, 66, 66, 1, 1, 1, 1, 1, 8, 8, 8, 15, 23, 23, 23, 23, 23, 8, 8, 1, 29, 29, 36, 36, 66, 66, 6, 1, 1, 1, 1, 8, 15, 15, 23, 23, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 282 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113507 none O=C(CCC1=NC=CS1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 1, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 100, 110, 157, 157, 157, 157, 8, 8, 8, 1, 1, 1, 1, 1, 4, 6, 6, 6, 6, 6, 1, 1, 8, 100, 100, 110, 110, 157, 157, 31, 8, 8, 8, 8, 1, 4, 4, 6, 6, 8, 8] 201 rigid atoms, others: [37, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 523 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113507 none O=C(CCC1=NC=CS1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 1, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 9, 3, 1, 1, 1, 1, 1, 1, 27, 27, 66, 66, 66, 157, 157, 157, 187, 201, 201, 201, 201, 201, 157, 157, 66, 9, 9, 3, 3, 1, 1, 27, 66, 66, 66, 66, 157, 187, 187, 201, 201, 66, 66] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 592 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113507 none O=C(CCC1=NC=CS1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 1, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 134, 138, 201, 201, 201, 201, 26, 26, 26, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 26, 134, 134, 138, 138, 201, 201, 72, 26, 26, 26, 26, 7, 4, 4, 2, 2, 26, 26] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 615 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113507 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113507/1 /scratch/stefan/7770410/working/building/REAL300020113507 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 620) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/620 `/scratch/stefan/7770410/working/3D/620' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=NC=CS1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113507.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113507 none O=C(CCC1=NC=CS1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 1, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 29, 38, 68, 68, 68, 68, 1, 1, 1, 1, 1, 8, 8, 8, 15, 23, 23, 23, 23, 23, 8, 8, 1, 29, 29, 38, 38, 68, 68, 6, 1, 1, 1, 1, 8, 15, 15, 23, 23, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 294 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113507 none O=C(CCC1=NC=CS1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 1, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 100, 112, 158, 158, 158, 158, 8, 8, 8, 1, 1, 1, 1, 1, 4, 6, 6, 6, 6, 6, 1, 1, 8, 100, 100, 112, 112, 158, 158, 31, 8, 8, 8, 8, 1, 4, 4, 6, 6, 8, 8] 201 rigid atoms, others: [37, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 533 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113507 none O=C(CCC1=NC=CS1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 1, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 9, 3, 1, 1, 1, 1, 1, 1, 27, 27, 68, 68, 68, 158, 158, 158, 187, 201, 201, 201, 201, 201, 158, 158, 68, 9, 9, 3, 3, 1, 1, 27, 68, 68, 68, 68, 158, 187, 187, 201, 201, 68, 68] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 589 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113507 none O=C(CCC1=NC=CS1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 1, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 135, 139, 201, 201, 201, 201, 26, 26, 26, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 26, 135, 135, 139, 139, 201, 201, 73, 26, 26, 26, 26, 7, 4, 4, 2, 2, 26, 26] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 618 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113507 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113507 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113507/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113507/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113507 Building REAL300020113508 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113508' /scratch/stefan/7770410/working/building/REAL300020113508 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113508 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113508/0 /scratch/stefan/7770410/working/building/REAL300020113508 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/621 `/scratch/stefan/7770410/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113508.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113508 none COCCC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 89, 73, 65, 27, 65, 27, 27, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 12, 12, 12, 12, 1, 1, 9, 101, 101, 101, 89, 89, 73, 73, 65, 65, 65, 65, 27, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 440 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113508 none COCCC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 183, 183, 107, 183, 107, 107, 56, 56, 56, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 56, 201, 201, 201, 201, 201, 183, 183, 183, 183, 183, 183, 107, 56, 56, 56, 56, 13, 6, 6, 4, 4, 56, 56] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 785 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113508 none COCCC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 29, 22, 17, 6, 17, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 31, 45, 54, 54, 54, 54, 9, 9, 1, 37, 37, 37, 29, 29, 22, 22, 17, 17, 17, 17, 6, 1, 1, 1, 1, 9, 31, 31, 45, 45, 1, 1] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 46, 47, 40, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 349 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113508 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113508/1 /scratch/stefan/7770410/working/building/REAL300020113508 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 622) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/622 `/scratch/stefan/7770410/working/3D/622' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113508.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113508/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113508 none COCCC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 89, 72, 65, 27, 65, 27, 27, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 12, 12, 12, 12, 1, 1, 9, 100, 100, 100, 89, 89, 72, 72, 65, 65, 65, 65, 27, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 438 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113508 none COCCC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 182, 182, 107, 182, 107, 107, 56, 56, 56, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 56, 201, 201, 201, 201, 201, 182, 182, 182, 182, 182, 182, 107, 56, 56, 56, 56, 12, 6, 6, 4, 4, 56, 56] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 789 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113508 none COCCC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 28, 22, 17, 6, 17, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 31, 45, 54, 54, 54, 54, 9, 9, 1, 35, 35, 35, 28, 28, 22, 22, 17, 17, 17, 17, 6, 1, 1, 1, 1, 9, 31, 31, 45, 45, 1, 1] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 46, 47, 40, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113508 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113508 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113508/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113508/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113508 Building REAL300020113509 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113509' /scratch/stefan/7770410/working/building/REAL300020113509 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113509 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113509/0 /scratch/stefan/7770410/working/building/REAL300020113509 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/623 `/scratch/stefan/7770410/working/3D/623' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)N1CCCC1=O) `REAL300020113509.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113509 none CCC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 73, 32, 32, 32, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 11, 11, 11, 11, 1, 1, 11, 73, 90, 90, 90, 90, 90, 94, 94, 94, 94, 94, 73, 32, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 90, 90, 90, 90, 90, 90] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 453 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113509 none CCC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [198, 181, 92, 92, 92, 47, 47, 47, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 47, 181, 201, 201, 201, 201, 201, 198, 198, 198, 198, 198, 181, 92, 47, 47, 47, 47, 9, 4, 4, 2, 2, 47, 47, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 813 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113509 none CCC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 18, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 36, 50, 53, 53, 53, 53, 11, 11, 1, 18, 26, 26, 26, 26, 26, 24, 24, 24, 24, 24, 18, 6, 1, 1, 1, 1, 11, 36, 36, 50, 50, 1, 1, 26, 26, 26, 26, 26, 26] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 44, 45, 21, 38, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51]) total number of confs: 314 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113509 none CCC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 1, 4, 9, 9, 9, 26, 26, 26, 90, 90, 90, 163, 201, 201, 201, 201, 201, 90, 90, 26, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 4, 9, 26, 26, 26, 26, 90, 163, 163, 201, 201, 26, 26, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 46, 47, 48, 49, 50, 51, 22, 23, 24, 25, 26, 27] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 761 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113509 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113509/1 /scratch/stefan/7770410/working/building/REAL300020113509 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 624) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/624 `/scratch/stefan/7770410/working/3D/624' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)N1CCCC1=O) `REAL300020113509.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113509/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113509 none CCC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 74, 33, 33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 74, 91, 91, 91, 91, 91, 95, 95, 95, 95, 95, 74, 33, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 91, 91, 91, 91, 91, 91] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 457 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113509 none CCC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [198, 181, 91, 91, 91, 46, 46, 46, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 46, 181, 201, 201, 201, 201, 201, 198, 198, 198, 198, 198, 181, 91, 46, 46, 46, 46, 8, 4, 4, 2, 2, 46, 46, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 817 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113509 none CCC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 18, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 35, 49, 54, 54, 54, 54, 11, 11, 1, 18, 26, 26, 26, 26, 26, 24, 24, 24, 24, 24, 18, 6, 1, 1, 1, 1, 11, 35, 35, 49, 49, 1, 1, 26, 26, 26, 26, 26, 26] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 44, 45, 21, 38, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51]) total number of confs: 315 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113509 none CCC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 1, 4, 9, 9, 9, 26, 26, 26, 91, 91, 91, 161, 201, 201, 201, 201, 201, 91, 91, 26, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 4, 9, 26, 26, 26, 26, 91, 161, 161, 201, 201, 26, 26, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 46, 47, 48, 49, 50, 51, 22, 23, 24, 25, 26, 27] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 759 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113509 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113509 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113509/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113509/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113509 Building REAL300020113510 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113510' /scratch/stefan/7770410/working/building/REAL300020113510 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113510 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113510/0 /scratch/stefan/7770410/working/building/REAL300020113510 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/625 `/scratch/stefan/7770410/working/3D/625' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1OC(C)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1C) `REAL300020113510.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113510 none CC1OC(C)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 63, 87, 98, 98, 98, 98, 13, 13, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 1, 1, 1, 13, 63, 63, 87, 87, 1, 1, 7, 7, 7, 7] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 46, 47, 40, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 382 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113510 none CC1OC(C)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 60, 60, 59, 59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 18, 18, 18, 18, 1, 1, 13, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 59, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 60, 60, 60, 60] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 208 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113510 none CC1OC(C)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 60, 60, 60, 160, 201, 201, 201, 201, 201, 60, 60, 7, 1, 1, 2, 2, 2, 1, 1, 2, 2, 2, 1, 3, 7, 7, 7, 7, 60, 160, 160, 201, 201, 7, 7, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 48, 35, 25, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51]) total number of confs: 789 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113510 none CC1OC(C)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 101, 101, 101, 20, 20, 20, 7, 4, 1, 1, 1, 1, 1, 1, 20, 20, 101, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 101, 101, 101, 101, 20, 7, 7, 4, 4, 101, 101, 201, 201, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 555 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113510 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113510/1 /scratch/stefan/7770410/working/building/REAL300020113510 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 626) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/626 `/scratch/stefan/7770410/working/3D/626' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1OC(C)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1C) `REAL300020113510.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113510 none CC1OC(C)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 65, 91, 99, 99, 99, 99, 13, 13, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 1, 1, 1, 13, 65, 65, 91, 91, 1, 1, 7, 7, 7, 7] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 46, 47, 40, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 394 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113510 none CC1OC(C)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 60, 60, 59, 59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 18, 18, 18, 18, 1, 1, 13, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 59, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 60, 60, 60, 60] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 208 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113510 none CC1OC(C)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 60, 60, 60, 158, 201, 201, 201, 201, 201, 60, 60, 7, 1, 1, 2, 2, 2, 1, 1, 2, 2, 2, 1, 3, 7, 7, 7, 7, 60, 158, 158, 201, 201, 7, 7, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 48, 35, 25, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51]) total number of confs: 789 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113510 none CC1OC(C)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 100, 100, 100, 19, 19, 19, 6, 4, 1, 1, 1, 1, 1, 1, 19, 19, 100, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 100, 100, 100, 100, 19, 6, 6, 4, 4, 100, 100, 201, 201, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 551 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113510 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113510 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113510/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113510/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113510 Building REAL300020113511 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113511' /scratch/stefan/7770410/working/building/REAL300020113511 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113511 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113511/0 /scratch/stefan/7770410/working/building/REAL300020113511 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/627 `/scratch/stefan/7770410/working/3D/627' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C)=C1CC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113511.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113511 none CC1=NNC(C)=C1CC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 28, 28, 27, 20, 6, 20, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 24, 37, 37, 37, 37, 37, 8, 8, 1, 28, 28, 28, 28, 28, 28, 28, 27, 27, 20, 20, 20, 20, 6, 1, 1, 1, 1, 8, 24, 24, 37, 37, 1, 1] 201 rigid atoms, others: [45, 44, 43, 12, 13, 14, 15, 16, 52, 46, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 266 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113511 none CC1=NNC(C)=C1CC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 103, 103, 103, 103, 86, 29, 86, 29, 29, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 103, 103, 103, 103, 103, 103, 103, 103, 103, 86, 86, 86, 86, 29, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [15, 47, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 436 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113511 none CC1=NNC(C)=C1CC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 17, 17, 17, 27, 27, 27, 104, 104, 104, 167, 201, 201, 201, 201, 201, 104, 104, 27, 2, 2, 2, 1, 2, 2, 2, 4, 4, 8, 8, 8, 8, 17, 27, 27, 27, 27, 104, 167, 167, 201, 201, 27, 27] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 732 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113511 none CC1=NNC(C)=C1CC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 182, 83, 182, 83, 83, 38, 38, 38, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 38, 201, 201, 201, 201, 201, 201, 201, 201, 201, 182, 182, 182, 182, 83, 38, 38, 38, 38, 9, 4, 4, 2, 2, 38, 38] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 795 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113511 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113511/1 /scratch/stefan/7770410/working/building/REAL300020113511 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 628) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/628 `/scratch/stefan/7770410/working/3D/628' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C)=C1CC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113511.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113511 none CC1=NNC(C)=C1CC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 28, 28, 27, 20, 6, 20, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 24, 37, 37, 37, 37, 37, 8, 8, 1, 28, 28, 28, 28, 28, 28, 28, 27, 27, 20, 20, 20, 20, 6, 1, 1, 1, 1, 8, 24, 24, 37, 37, 1, 1] 201 rigid atoms, others: [45, 44, 43, 12, 13, 14, 15, 16, 52, 46, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 266 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113511 none CC1=NNC(C)=C1CC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 102, 102, 102, 102, 86, 29, 86, 29, 29, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 102, 102, 102, 102, 102, 102, 102, 102, 102, 86, 86, 86, 86, 29, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [15, 47, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 430 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113511 none CC1=NNC(C)=C1CC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 17, 17, 17, 26, 26, 26, 104, 104, 104, 167, 201, 201, 201, 201, 201, 104, 104, 26, 2, 2, 2, 1, 2, 2, 2, 4, 4, 8, 8, 8, 8, 17, 26, 26, 26, 26, 104, 167, 167, 201, 201, 26, 26] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 730 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113511 none CC1=NNC(C)=C1CC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 183, 85, 183, 85, 85, 39, 39, 39, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 39, 201, 201, 201, 201, 201, 201, 201, 201, 201, 183, 183, 183, 183, 85, 39, 39, 39, 39, 9, 4, 4, 2, 2, 39, 39] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 790 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113511 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113511 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113511/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113511/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113511 Building REAL300020113512 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113512' /scratch/stefan/7770410/working/building/REAL300020113512 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113512 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113512/0 /scratch/stefan/7770410/working/building/REAL300020113512 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/629 `/scratch/stefan/7770410/working/3D/629' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CNN=C1C1=CC=CO1) `REAL300020113512.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113512 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CNN=C1C1=CC=CO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 34, 84, 84, 84, 84, 84, 144, 144, 144, 144, 34, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 84, 84, 144, 144, 144] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 296 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113512 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CNN=C1C1=CC=CO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 18, 18, 47, 47, 47, 144, 144, 144, 186, 201, 201, 201, 201, 201, 144, 144, 47, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 18, 47, 47, 47, 47, 144, 186, 186, 201, 201, 47, 47, 7, 7, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 571 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113512 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CNN=C1C1=CC=CO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 53, 53, 53, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 53, 115, 201, 201, 201, 201, 201, 201, 201, 201, 201, 115, 53, 53, 53, 53, 11, 6, 6, 4, 4, 53, 53, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 468 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113512 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CNN=C1C1=CC=CO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 48, 52, 52, 52, 52, 11, 11, 1, 6, 20, 20, 20, 20, 20, 47, 47, 47, 47, 6, 1, 1, 1, 1, 11, 33, 33, 48, 48, 1, 1, 20, 20, 47, 47, 47] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113512 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CNN=C1C1=CC=CO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 20, 20, 20, 84, 84, 84, 164, 196, 200, 200, 200, 200, 84, 84, 20, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 20, 20, 20, 20, 84, 164, 164, 196, 196, 20, 20, 1, 1, 7, 7, 7] 201 rigid atoms, others: [1, 41, 42, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 697 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113512 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113512/1 /scratch/stefan/7770410/working/building/REAL300020113512 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 630) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/630 `/scratch/stefan/7770410/working/3D/630' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CNN=C1C1=CC=CO1) `REAL300020113512.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113512 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CNN=C1C1=CC=CO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 33, 83, 83, 83, 83, 83, 145, 145, 145, 145, 33, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 83, 83, 145, 145, 145] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 298 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113512 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CNN=C1C1=CC=CO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 7, 19, 19, 47, 47, 47, 145, 145, 145, 186, 201, 201, 201, 201, 201, 145, 145, 47, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 19, 47, 47, 47, 47, 145, 186, 186, 201, 201, 47, 47, 7, 7, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 567 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113512 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CNN=C1C1=CC=CO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 53, 53, 53, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 53, 116, 201, 201, 201, 201, 201, 201, 201, 201, 201, 116, 53, 53, 53, 53, 10, 6, 6, 4, 4, 53, 53, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 469 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113512 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CNN=C1C1=CC=CO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 34, 49, 53, 53, 53, 53, 11, 11, 1, 6, 21, 21, 21, 21, 21, 47, 47, 47, 47, 6, 1, 1, 1, 1, 11, 34, 34, 49, 49, 1, 1, 21, 21, 47, 47, 47] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113512 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CNN=C1C1=CC=CO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 21, 21, 21, 83, 83, 83, 163, 196, 200, 200, 200, 200, 83, 83, 21, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 8, 21, 21, 21, 21, 83, 163, 163, 196, 196, 21, 21, 1, 1, 7, 7, 7] 201 rigid atoms, others: [1, 41, 42, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 705 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113512 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113512 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113512/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113512/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113512 Building REAL300020113513 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113513' /scratch/stefan/7770410/working/building/REAL300020113513 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113513 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113513/0 /scratch/stefan/7770410/working/building/REAL300020113513 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/631 `/scratch/stefan/7770410/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=COC2=C(F)C=C1) `REAL300020113513.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113513 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=COC2=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 1, 1, 6, 17, 33, 33, 33, 33, 33, 33, 33, 33, 33, 17, 6, 6, 6, 6, 1, 8, 8, 10, 10, 6, 6, 33, 33, 33, 33] 54 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 107 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113513 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=COC2=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 23, 23, 23, 11, 11, 11, 5, 2, 1, 1, 1, 1, 1, 1, 11, 11, 23, 35, 54, 54, 54, 54, 54, 54, 54, 54, 54, 35, 23, 23, 23, 23, 11, 5, 5, 2, 2, 23, 23, 54, 54, 54, 54] 54 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 140 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113513 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=COC2=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 16, 23, 23, 23, 23, 23, 6, 6, 1, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 6, 16, 16, 23, 23, 1, 1, 23, 23, 23, 23] 54 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113513 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=COC2=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 23, 23, 23, 33, 33, 33, 48, 54, 54, 54, 54, 54, 33, 33, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 23, 23, 23, 23, 33, 48, 48, 54, 54, 23, 23, 1, 1, 1, 1] 54 rigid atoms, others: [1, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 192 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113513 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113513/1 /scratch/stefan/7770410/working/building/REAL300020113513 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 632) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/632 `/scratch/stefan/7770410/working/3D/632' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=COC2=C(F)C=C1) `REAL300020113513.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113513/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113513 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=COC2=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 1, 1, 6, 17, 33, 33, 33, 33, 33, 33, 33, 33, 33, 17, 6, 6, 6, 6, 1, 8, 8, 10, 10, 6, 6, 33, 33, 33, 33] 54 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 107 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113513 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=COC2=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 23, 23, 23, 11, 11, 11, 5, 2, 1, 1, 1, 1, 1, 1, 11, 11, 23, 35, 54, 54, 54, 54, 54, 54, 54, 54, 54, 35, 23, 23, 23, 23, 11, 5, 5, 2, 2, 23, 23, 54, 54, 54, 54] 54 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 140 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113513 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=COC2=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 16, 23, 23, 23, 23, 23, 6, 6, 1, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 6, 16, 16, 23, 23, 1, 1, 23, 23, 23, 23] 54 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113513 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=COC2=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 23, 23, 23, 33, 33, 33, 48, 54, 54, 54, 54, 54, 33, 33, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 23, 23, 23, 23, 33, 48, 48, 54, 54, 23, 23, 1, 1, 1, 1] 54 rigid atoms, others: [1, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 192 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113513 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113513 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113513/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113513/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113513 Building REAL300020113514 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113514' /scratch/stefan/7770410/working/building/REAL300020113514 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113514 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113514/0 /scratch/stefan/7770410/working/building/REAL300020113514 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/633 `/scratch/stefan/7770410/working/3D/633' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(CC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113514.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113514 none COC(CC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 9, 6, 9, 22, 22, 22, 22, 22, 22, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 37, 53, 63, 63, 63, 63, 11, 11, 1, 10, 10, 10, 9, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 37, 37, 53, 53, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 325 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113514 none COC(CC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 59, 41, 59, 98, 98, 98, 98, 98, 98, 41, 41, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 60, 60, 60, 59, 98, 98, 98, 98, 98, 98, 98, 41, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 445 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113514 none COC(CC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 22, 22, 22, 98, 98, 98, 167, 201, 201, 201, 201, 201, 98, 98, 22, 6, 6, 6, 5, 1, 1, 1, 1, 1, 1, 1, 8, 22, 22, 22, 22, 98, 167, 167, 201, 201, 22, 22] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 9, 39, 34, 35, 36, 38, 37] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 735 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113514 none COC(CC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [170, 168, 132, 168, 201, 201, 201, 201, 201, 201, 132, 132, 62, 62, 62, 14, 14, 14, 4, 4, 1, 1, 1, 1, 1, 1, 14, 14, 62, 170, 170, 170, 168, 201, 201, 201, 201, 201, 201, 201, 132, 62, 62, 62, 62, 14, 4, 4, 4, 4, 62, 62] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 748 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113514 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113514/1 /scratch/stefan/7770410/working/building/REAL300020113514 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 634) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/634 `/scratch/stefan/7770410/working/3D/634' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(CC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113514.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113514/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113514 none COC(CC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 9, 6, 9, 22, 22, 22, 22, 22, 22, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 36, 52, 63, 63, 63, 63, 11, 11, 1, 10, 10, 10, 9, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 36, 36, 52, 52, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 324 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113514 none COC(CC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 58, 41, 58, 100, 100, 100, 100, 100, 100, 41, 41, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 59, 59, 59, 58, 100, 100, 100, 100, 100, 100, 100, 41, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 451 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113514 none COC(CC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 22, 22, 22, 100, 100, 100, 167, 201, 201, 201, 201, 201, 100, 100, 22, 6, 6, 6, 5, 1, 1, 1, 1, 1, 1, 1, 8, 22, 22, 22, 22, 100, 167, 167, 201, 201, 22, 22] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 9, 39, 34, 35, 36, 38, 37] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 725 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113514 none COC(CC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [169, 167, 132, 167, 201, 201, 201, 201, 201, 201, 132, 132, 64, 64, 64, 15, 15, 15, 4, 4, 1, 1, 1, 1, 1, 1, 15, 15, 64, 169, 169, 169, 167, 201, 201, 201, 201, 201, 201, 201, 132, 64, 64, 64, 64, 15, 4, 4, 4, 4, 64, 64] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 748 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113514 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113514 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113514/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113514/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113514 Building REAL300020113515 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113515' /scratch/stefan/7770410/working/building/REAL300020113515 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113515 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113515/0 /scratch/stefan/7770410/working/building/REAL300020113515 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/635 `/scratch/stefan/7770410/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(CC)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113515.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113515 none CCC(C)(CC)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 65, 38, 65, 65, 77, 38, 38, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 79, 79, 79, 79, 79, 65, 65, 65, 79, 79, 79, 79, 79, 38, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11] 201 rigid atoms, others: [11, 43, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 453 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113515 none CCC(C)(CC)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 171, 91, 171, 171, 201, 91, 91, 62, 62, 62, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 62, 201, 201, 201, 201, 201, 171, 171, 171, 201, 201, 201, 201, 201, 91, 62, 62, 62, 62, 13, 6, 6, 4, 4, 62, 62] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 993 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113515 none CCC(C)(CC)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 13, 6, 13, 13, 15, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 39, 55, 62, 62, 62, 62, 11, 11, 1, 17, 17, 17, 17, 17, 13, 13, 13, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 11, 39, 39, 55, 55, 1, 1] 201 rigid atoms, others: [49, 39, 8, 9, 10, 11, 12, 48, 40, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 354 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113515 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113515/1 /scratch/stefan/7770410/working/building/REAL300020113515 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 636) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/636 `/scratch/stefan/7770410/working/3D/636' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(CC)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113515.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113515/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113515 none CCC(C)(CC)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 65, 38, 65, 65, 75, 38, 38, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 77, 77, 77, 77, 77, 65, 65, 65, 77, 77, 77, 77, 77, 38, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11] 201 rigid atoms, others: [11, 43, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 429 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113515 none CCC(C)(CC)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 171, 91, 171, 171, 201, 91, 91, 62, 62, 62, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 62, 201, 201, 201, 201, 201, 171, 171, 171, 201, 201, 201, 201, 201, 91, 62, 62, 62, 62, 12, 6, 6, 4, 4, 62, 62] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 994 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113515 none CCC(C)(CC)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 13, 6, 13, 13, 15, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 38, 54, 61, 61, 61, 61, 11, 11, 1, 17, 17, 17, 17, 17, 13, 13, 13, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 11, 38, 38, 54, 54, 1, 1] 201 rigid atoms, others: [49, 39, 8, 9, 10, 11, 12, 48, 40, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 351 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113515 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113515 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113515/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113515/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113515 Building REAL300020113516 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113516' /scratch/stefan/7770410/working/building/REAL300020113516 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113516 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113516/0 /scratch/stefan/7770410/working/building/REAL300020113516 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/637 `/scratch/stefan/7770410/working/3D/637' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020113516.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113516 none CNC(=O)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 12, 24, 12, 12, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 28, 41, 43, 43, 43, 43, 10, 10, 1, 12, 24, 24, 24, 24, 12, 12, 12, 5, 1, 1, 1, 1, 10, 28, 28, 41, 41, 1, 1, 12] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48]) total number of confs: 228 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113516 none CNC(=O)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 60, 99, 60, 60, 60, 60, 20, 20, 20, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 10, 60, 99, 99, 99, 99, 60, 60, 60, 20, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 60] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 290 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113516 none CNC(=O)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 60, 60, 60, 127, 176, 178, 178, 178, 178, 60, 60, 12, 1, 5, 5, 5, 5, 1, 1, 1, 5, 12, 12, 12, 12, 60, 127, 127, 176, 176, 12, 12, 1] 201 rigid atoms, others: [33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 48, 28] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 722 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113516 none CNC(=O)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 178, 201, 178, 178, 178, 178, 69, 69, 69, 44, 44, 44, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 44, 178, 201, 201, 201, 201, 178, 178, 178, 69, 44, 44, 44, 44, 11, 6, 6, 4, 4, 44, 44, 178] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 449 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113516 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113516/1 /scratch/stefan/7770410/working/building/REAL300020113516 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 638) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/638 `/scratch/stefan/7770410/working/3D/638' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020113516.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113516 none CNC(=O)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 12, 24, 12, 12, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 28, 41, 43, 43, 43, 43, 10, 10, 1, 12, 24, 24, 24, 24, 12, 12, 12, 5, 1, 1, 1, 1, 10, 28, 28, 41, 41, 1, 1, 12] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48]) total number of confs: 228 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113516 none CNC(=O)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 60, 99, 60, 60, 60, 60, 20, 20, 20, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 10, 60, 99, 99, 99, 99, 60, 60, 60, 20, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 60] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 290 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113516 none CNC(=O)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 60, 60, 60, 127, 176, 178, 178, 178, 178, 60, 60, 12, 1, 5, 5, 5, 5, 1, 1, 1, 5, 12, 12, 12, 12, 60, 127, 127, 176, 176, 12, 12, 1] 201 rigid atoms, others: [33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 48, 28] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 722 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113516 none CNC(=O)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 178, 201, 178, 178, 178, 178, 69, 69, 69, 44, 44, 44, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 44, 178, 201, 201, 201, 201, 178, 178, 178, 69, 44, 44, 44, 44, 11, 6, 6, 4, 4, 44, 44, 178] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 449 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113516 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113516 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113516/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113516/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113516 Building REAL300020113517 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113517' /scratch/stefan/7770410/working/building/REAL300020113517 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113517 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113517/0 /scratch/stefan/7770410/working/building/REAL300020113517 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/639 `/scratch/stefan/7770410/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC(F)=C1) `REAL300020113517.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113517 none CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 30, 30, 30, 10, 10, 10, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 10, 58, 110, 110, 110, 110, 110, 110, 58, 58, 58, 58, 30, 10, 10, 10, 10, 1, 7, 7, 9, 9, 10, 10, 110, 110, 110, 110] 201 rigid atoms, others: [37, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 342 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113517 none CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [135, 90, 90, 90, 48, 48, 48, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 48, 135, 201, 201, 201, 201, 201, 201, 135, 135, 135, 135, 90, 48, 48, 48, 48, 12, 6, 6, 4, 4, 48, 48, 201, 201, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 625 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113517 none CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 30, 44, 47, 47, 47, 47, 10, 10, 1, 13, 30, 30, 30, 30, 30, 30, 13, 13, 13, 13, 6, 1, 1, 1, 1, 10, 30, 30, 44, 44, 1, 1, 30, 30, 30, 30] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 42, 43, 20, 36] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113517 none CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 11, 11, 11, 30, 30, 30, 110, 110, 110, 169, 201, 201, 201, 201, 201, 110, 110, 30, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 30, 30, 30, 30, 110, 169, 169, 201, 201, 30, 30, 1, 1, 1, 1] 201 rigid atoms, others: [1, 44, 45, 46, 47, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 683 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113517 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113517/1 /scratch/stefan/7770410/working/building/REAL300020113517 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 640) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/640 `/scratch/stefan/7770410/working/3D/640' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC(F)=C1) `REAL300020113517.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113517/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113517 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 30, 30, 30, 10, 10, 10, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 10, 58, 107, 107, 107, 107, 107, 107, 58, 58, 58, 58, 30, 10, 10, 10, 10, 1, 7, 7, 9, 9, 10, 10, 107, 107, 107, 107] 201 rigid atoms, others: [37, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 337 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113517 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [132, 90, 90, 90, 48, 48, 48, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 48, 132, 201, 201, 201, 201, 201, 201, 132, 132, 132, 132, 90, 48, 48, 48, 48, 12, 6, 6, 4, 4, 48, 48, 201, 201, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 616 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113517 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 29, 43, 47, 47, 47, 47, 10, 10, 1, 13, 30, 30, 30, 30, 30, 30, 13, 13, 13, 13, 6, 1, 1, 1, 1, 10, 29, 29, 43, 43, 1, 1, 30, 30, 30, 30] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 42, 43, 20, 36] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113517 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 11, 11, 11, 30, 30, 30, 107, 107, 107, 168, 201, 201, 201, 201, 201, 107, 107, 30, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 30, 30, 30, 30, 107, 168, 168, 201, 201, 30, 30, 1, 1, 1, 1] 201 rigid atoms, others: [1, 44, 45, 46, 47, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 692 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113517 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113517 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113517/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113517/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113517 Building REAL300020113518 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113518' /scratch/stefan/7770410/working/building/REAL300020113518 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113518 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113518/0 /scratch/stefan/7770410/working/building/REAL300020113518 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/641 `/scratch/stefan/7770410/working/3D/641' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1=CC=CO1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113518.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113518 none C[C@H](NC(=O)C1=CC=CO1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 6, 28, 28, 37, 37, 37, 37, 37, 37, 37, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 30, 42, 42, 42, 42, 42, 12, 12, 1, 28, 28, 28, 37, 37, 37, 37, 6, 1, 1, 1, 1, 12, 30, 30, 42, 42, 1, 1] 201 rigid atoms, others: [48, 38, 39, 40, 41, 13, 14, 15, 16, 17, 47, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 298 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113518 none C[C@H](NC(=O)C1=CC=CO1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [121, 46, 121, 121, 130, 130, 130, 130, 130, 130, 130, 46, 46, 12, 12, 12, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 12, 121, 121, 121, 130, 130, 130, 130, 46, 12, 12, 12, 12, 1, 6, 6, 8, 8, 12, 12] 201 rigid atoms, others: [42, 16, 17, 18, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 511 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113518 none C[C@H](NC(=O)C1=CC=CO1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 3, 2, 1, 2, 1, 1, 1, 1, 1, 3, 12, 12, 12, 37, 37, 37, 130, 130, 130, 174, 201, 201, 201, 201, 201, 130, 130, 37, 3, 3, 3, 2, 1, 1, 1, 12, 37, 37, 37, 37, 130, 174, 174, 201, 201, 37, 37] 201 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 36] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 631 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113518 none C[C@H](NC(=O)C1=CC=CO1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [198, 104, 198, 198, 201, 201, 201, 201, 201, 201, 201, 104, 104, 40, 40, 40, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 40, 198, 198, 198, 201, 201, 201, 201, 104, 40, 40, 40, 40, 8, 4, 4, 2, 2, 40, 40] 201 rigid atoms, others: [21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 740 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113518 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113518/1 /scratch/stefan/7770410/working/building/REAL300020113518 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 642) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/642 `/scratch/stefan/7770410/working/3D/642' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1=CC=CO1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113518.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113518/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113518 none C[C@H](NC(=O)C1=CC=CO1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 6, 28, 28, 37, 37, 37, 37, 37, 37, 37, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 31, 43, 43, 43, 43, 43, 13, 13, 1, 28, 28, 28, 37, 37, 37, 37, 6, 1, 1, 1, 1, 13, 31, 31, 43, 43, 1, 1] 201 rigid atoms, others: [48, 38, 39, 40, 41, 13, 14, 15, 16, 17, 47, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 299 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113518 none C[C@H](NC(=O)C1=CC=CO1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [122, 47, 122, 122, 131, 131, 131, 131, 131, 131, 131, 47, 47, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 122, 122, 122, 131, 131, 131, 131, 47, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [42, 16, 17, 18, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 513 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113518 none C[C@H](NC(=O)C1=CC=CO1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 3, 2, 1, 2, 1, 1, 1, 1, 1, 3, 12, 12, 12, 37, 37, 37, 131, 131, 131, 174, 201, 201, 201, 201, 201, 131, 131, 37, 3, 3, 3, 2, 1, 1, 1, 12, 37, 37, 37, 37, 131, 174, 174, 201, 201, 37, 37] 201 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 36] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 626 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113518 none C[C@H](NC(=O)C1=CC=CO1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [198, 104, 198, 198, 201, 201, 201, 201, 201, 201, 201, 104, 104, 40, 40, 40, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 40, 198, 198, 198, 201, 201, 201, 201, 104, 40, 40, 40, 40, 8, 4, 4, 2, 2, 40, 40] 201 rigid atoms, others: [21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 737 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113518 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113518 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113518/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113518/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113518 Building REAL300020113519 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113519' /scratch/stefan/7770410/working/building/REAL300020113519 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113519 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113519/0 /scratch/stefan/7770410/working/building/REAL300020113519 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/643 `/scratch/stefan/7770410/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2=CC=CC(F)=C2O1) `REAL300020113519.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113519 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2=CC=CC(F)=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 14, 14, 14, 14, 1, 1, 11, 46, 99, 99, 99, 99, 99, 99, 99, 99, 99, 46, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 99, 99, 99, 99, 99, 99] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 329 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113519 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2=CC=CC(F)=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 78, 78, 78, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 78, 189, 201, 201, 201, 201, 201, 201, 201, 201, 201, 189, 78, 78, 78, 78, 14, 6, 6, 4, 4, 78, 78, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 578 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113519 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2=CC=CC(F)=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 43, 63, 78, 78, 78, 78, 11, 11, 1, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 11, 43, 43, 63, 63, 1, 1, 20, 20, 20, 20, 20, 20] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 338 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113519 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2=CC=CC(F)=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 20, 20, 20, 99, 99, 99, 180, 201, 201, 201, 201, 201, 99, 99, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 20, 20, 20, 20, 99, 180, 180, 201, 201, 20, 20, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 681 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113519 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113519/1 /scratch/stefan/7770410/working/building/REAL300020113519 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 644) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/644 `/scratch/stefan/7770410/working/3D/644' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2=CC=CC(F)=C2O1) `REAL300020113519.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113519/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113519 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2=CC=CC(F)=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 14, 14, 14, 14, 1, 1, 11, 46, 99, 99, 99, 99, 99, 99, 99, 99, 99, 46, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 99, 99, 99, 99, 99, 99] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 329 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113519 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2=CC=CC(F)=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 79, 79, 79, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 79, 189, 201, 201, 201, 201, 201, 201, 201, 201, 201, 189, 79, 79, 79, 79, 15, 6, 6, 4, 4, 79, 79, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 577 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113519 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2=CC=CC(F)=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 43, 63, 78, 78, 78, 78, 11, 11, 1, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 11, 43, 43, 63, 63, 1, 1, 20, 20, 20, 20, 20, 20] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 338 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113519 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2=CC=CC(F)=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 20, 20, 20, 99, 99, 99, 180, 201, 201, 201, 201, 201, 99, 99, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 20, 20, 20, 20, 99, 180, 180, 201, 201, 20, 20, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 681 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113519 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113519 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113519/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113519/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113519 Building REAL300020113520 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113520' /scratch/stefan/7770410/working/building/REAL300020113520 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113520 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113520/0 /scratch/stefan/7770410/working/building/REAL300020113520 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 645) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/645 `/scratch/stefan/7770410/working/3D/645' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CC=CC(F)=C2O1) `REAL300020113520.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113520 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CC=CC(F)=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 15, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 8, 8, 8, 1, 1, 1, 1, 1, 9, 11, 17, 17, 17, 17, 1, 1, 8, 29, 89, 89, 89, 89, 89, 89, 89, 89, 89, 29, 8, 8, 8, 8, 1, 9, 9, 11, 11, 8, 8, 89, 89, 89, 89] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 205 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113520 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CC=CC(F)=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 15, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [155, 155, 75, 75, 75, 24, 24, 24, 6, 4, 1, 1, 1, 1, 1, 1, 24, 24, 75, 155, 201, 201, 201, 201, 201, 201, 201, 201, 201, 155, 75, 75, 75, 75, 24, 6, 6, 4, 4, 75, 75, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 506 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113520 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CC=CC(F)=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 15, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 41, 51, 66, 66, 66, 66, 8, 8, 1, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 1, 1, 1, 1, 8, 41, 41, 51, 51, 1, 1, 28, 28, 28, 28] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113520 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CC=CC(F)=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 15, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 28, 28, 28, 89, 89, 89, 174, 201, 201, 201, 201, 201, 89, 89, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 28, 28, 28, 28, 89, 174, 174, 201, 201, 28, 28, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 723 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113520 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113520/1 /scratch/stefan/7770410/working/building/REAL300020113520 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 646) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/646 `/scratch/stefan/7770410/working/3D/646' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CC=CC(F)=C2O1) `REAL300020113520.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113520/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113520 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CC=CC(F)=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 15, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 8, 8, 8, 1, 1, 1, 1, 1, 9, 11, 17, 17, 17, 17, 1, 1, 8, 29, 88, 88, 88, 88, 88, 88, 88, 88, 88, 29, 8, 8, 8, 8, 1, 9, 9, 11, 11, 8, 8, 88, 88, 88, 88] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 204 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113520 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CC=CC(F)=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 15, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [153, 153, 74, 74, 74, 24, 24, 24, 6, 4, 1, 1, 1, 1, 1, 1, 24, 24, 74, 153, 201, 201, 201, 201, 201, 201, 201, 201, 201, 153, 74, 74, 74, 74, 24, 6, 6, 4, 4, 74, 74, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 510 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113520 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CC=CC(F)=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 15, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 41, 51, 64, 64, 64, 64, 8, 8, 1, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 1, 1, 1, 1, 8, 41, 41, 51, 51, 1, 1, 28, 28, 28, 28] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113520 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CC=CC(F)=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 15, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 28, 28, 28, 88, 88, 88, 175, 201, 201, 201, 201, 201, 88, 88, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 28, 28, 28, 28, 88, 175, 175, 201, 201, 28, 28, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 728 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113520 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113520 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113520/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113520/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113520 Building REAL300020113521 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113521' /scratch/stefan/7770410/working/building/REAL300020113521 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113521 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113521/0 /scratch/stefan/7770410/working/building/REAL300020113521 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/647 `/scratch/stefan/7770410/working/3D/647' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCS1(=O)=O) `REAL300020113521.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113521 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCS1(=O)=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 14, 11, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 12, 12, 12, 1, 1, 1, 1, 1, 8, 10, 15, 15, 15, 15, 1, 1, 12, 46, 99, 99, 99, 99, 99, 99, 46, 12, 12, 12, 12, 1, 8, 8, 10, 10, 12, 12, 99, 99, 99, 99, 99, 99, 99] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 333 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113521 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCS1(=O)=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 14, 11, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [182, 182, 89, 89, 89, 16, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 89, 182, 201, 201, 201, 201, 201, 201, 182, 89, 89, 89, 89, 16, 6, 6, 4, 4, 89, 89, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 574 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113521 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCS1(=O)=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 14, 11, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 50, 72, 90, 90, 90, 90, 12, 12, 1, 6, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 12, 50, 50, 72, 72, 1, 1, 21, 21, 21, 21, 21, 21, 21] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 380 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113521 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCS1(=O)=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 14, 11, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 21, 21, 21, 99, 99, 99, 183, 201, 201, 201, 201, 201, 99, 99, 21, 1, 1, 1, 1, 1, 1, 1, 6, 21, 21, 21, 21, 99, 183, 183, 201, 201, 21, 21, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 38, 39, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 652 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113521 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113521/1 /scratch/stefan/7770410/working/building/REAL300020113521 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 648) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/648 `/scratch/stefan/7770410/working/3D/648' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCS1(=O)=O) `REAL300020113521.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113521/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113521 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCS1(=O)=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 14, 11, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 12, 12, 12, 1, 1, 1, 1, 1, 8, 10, 15, 15, 15, 15, 1, 1, 12, 46, 99, 99, 99, 99, 99, 99, 46, 12, 12, 12, 12, 1, 8, 8, 10, 10, 12, 12, 99, 99, 99, 99, 99, 99, 99] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 333 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113521 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCS1(=O)=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 14, 11, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [182, 182, 90, 90, 90, 16, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 90, 182, 201, 201, 201, 201, 201, 201, 182, 90, 90, 90, 90, 16, 6, 6, 4, 4, 90, 90, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 572 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113521 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCS1(=O)=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 14, 11, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 50, 72, 90, 90, 90, 90, 12, 12, 1, 6, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 12, 50, 50, 72, 72, 1, 1, 21, 21, 21, 21, 21, 21, 21] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 380 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113521 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCS1(=O)=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 14, 11, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 21, 21, 21, 99, 99, 99, 183, 201, 201, 201, 201, 201, 99, 99, 21, 1, 1, 1, 1, 1, 1, 1, 6, 21, 21, 21, 21, 99, 183, 183, 201, 201, 21, 21, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 38, 39, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 652 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113521 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113521 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113521/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113521/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113521 Building REAL300020113522 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113522' /scratch/stefan/7770410/working/building/REAL300020113522 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113522 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113522/0 /scratch/stefan/7770410/working/building/REAL300020113522 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/649 `/scratch/stefan/7770410/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NOC2=C1COCC2) `REAL300020113522.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113522 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NOC2=C1COCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 12, 1, 1, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 20, 20, 20, 20, 1, 1, 13, 53, 82, 82, 82, 82, 82, 82, 82, 82, 53, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 82, 82, 82, 82, 82, 82] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 249 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113522 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NOC2=C1COCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 12, 1, 1, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 116, 116, 116, 21, 21, 21, 6, 4, 1, 1, 1, 1, 1, 1, 21, 21, 116, 200, 201, 201, 201, 201, 201, 201, 201, 201, 200, 116, 116, 116, 116, 21, 6, 6, 4, 4, 116, 116, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 545 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113522 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NOC2=C1COCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 12, 1, 1, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 67, 90, 115, 115, 115, 115, 13, 13, 1, 6, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 13, 67, 67, 90, 90, 1, 1, 15, 15, 15, 15, 15, 15] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 426 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113522 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NOC2=C1COCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 12, 1, 1, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 15, 15, 15, 82, 82, 82, 163, 201, 201, 201, 201, 201, 82, 82, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 15, 15, 15, 15, 82, 163, 163, 201, 201, 15, 15, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 733 number of broken/clashed sets: 2 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113522 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113522/1 /scratch/stefan/7770410/working/building/REAL300020113522 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 650) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/650 `/scratch/stefan/7770410/working/3D/650' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NOC2=C1COCC2) `REAL300020113522.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113522/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113522 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NOC2=C1COCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 12, 1, 1, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 20, 20, 20, 20, 1, 1, 13, 53, 82, 82, 82, 82, 82, 82, 82, 82, 53, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 82, 82, 82, 82, 82, 82] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 249 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113522 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NOC2=C1COCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 12, 1, 1, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 115, 115, 115, 21, 21, 21, 6, 4, 1, 1, 1, 1, 1, 1, 21, 21, 115, 200, 201, 201, 201, 201, 201, 201, 201, 201, 200, 115, 115, 115, 115, 21, 6, 6, 4, 4, 115, 115, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 545 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113522 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NOC2=C1COCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 12, 1, 1, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 67, 90, 115, 115, 115, 115, 13, 13, 1, 6, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 13, 67, 67, 90, 90, 1, 1, 15, 15, 15, 15, 15, 15] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 426 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113522 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NOC2=C1COCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 12, 1, 1, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 15, 15, 15, 82, 82, 82, 163, 201, 201, 201, 201, 201, 82, 82, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 15, 15, 15, 15, 82, 163, 163, 201, 201, 15, 15, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 733 number of broken/clashed sets: 2 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113522 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113522 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113522/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113522/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113522 Building REAL300020113523 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113523' /scratch/stefan/7770410/working/building/REAL300020113523 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113523 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113523/0 /scratch/stefan/7770410/working/building/REAL300020113523 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/651 `/scratch/stefan/7770410/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2=CNN=C2C1) `REAL300020113523.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113523 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2=CNN=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 8, 8, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 10, 32, 97, 97, 97, 97, 97, 97, 97, 97, 32, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 97, 97, 97, 97, 97, 97, 97, 97, 97] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 285 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113523 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2=CNN=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 8, 8, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 50, 50, 50, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 50, 103, 201, 201, 201, 201, 201, 201, 201, 201, 103, 50, 50, 50, 50, 11, 6, 6, 4, 4, 50, 50, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 603 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113523 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2=CNN=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 8, 8, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 31, 45, 49, 49, 49, 49, 10, 10, 1, 6, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 10, 31, 31, 45, 45, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113523 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2=CNN=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 8, 8, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 9, 21, 21, 21, 97, 97, 97, 158, 201, 201, 201, 201, 201, 97, 97, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 21, 21, 21, 21, 97, 158, 158, 201, 201, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 729 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113523 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113523/1 /scratch/stefan/7770410/working/building/REAL300020113523 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 652) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/652 `/scratch/stefan/7770410/working/3D/652' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2=CNN=C2C1) `REAL300020113523.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113523/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113523 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2=CNN=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 8, 8, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 10, 33, 96, 96, 96, 96, 96, 96, 96, 96, 33, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 96, 96, 96, 96, 96, 96, 96, 96, 96] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 283 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113523 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2=CNN=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 8, 8, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 50, 50, 50, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 50, 105, 201, 201, 201, 201, 201, 201, 201, 201, 105, 50, 50, 50, 50, 11, 6, 6, 4, 4, 50, 50, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 603 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113523 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2=CNN=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 8, 8, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 31, 45, 50, 50, 50, 50, 10, 10, 1, 6, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 10, 31, 31, 45, 45, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113523 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2=CNN=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 8, 8, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 8, 20, 20, 20, 96, 96, 96, 157, 201, 201, 201, 201, 201, 96, 96, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 20, 20, 20, 20, 96, 157, 157, 201, 201, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 736 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113523 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113523 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113523/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113523/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113523 Building REAL300020113524 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113524' /scratch/stefan/7770410/working/building/REAL300020113524 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113524 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113524/0 /scratch/stefan/7770410/working/building/REAL300020113524 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/653 `/scratch/stefan/7770410/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C2CC2)N=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113524.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113524 none CN1N=C(C2CC2)N=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 9, 9, 9, 16, 29, 29, 29, 52, 52, 52, 119, 119, 119, 179, 201, 201, 201, 201, 201, 119, 119, 52, 9, 9, 9, 1, 1, 1, 1, 1, 16, 16, 29, 52, 52, 52, 52, 119, 179, 179, 201, 201, 52, 52] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 35, 36] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 724 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113524 none CN1N=C(C2CC2)N=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 124, 124, 124, 124, 201, 201, 124, 124, 52, 52, 52, 33, 33, 33, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 33, 124, 124, 124, 201, 201, 201, 201, 201, 124, 124, 52, 33, 33, 33, 33, 8, 4, 4, 2, 2, 33, 33] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 782 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113524 none CN1N=C(C2CC2)N=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 52, 52, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 20, 32, 32, 32, 32, 32, 7, 7, 1, 16, 16, 16, 52, 52, 52, 52, 52, 16, 16, 5, 1, 1, 1, 1, 7, 20, 20, 32, 32, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 16, 49, 50, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 292 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113524 none CN1N=C(C2CC2)N=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 1, 1, 1, 3, 7, 7, 7, 16, 16, 16, 52, 52, 52, 99, 122, 122, 122, 122, 122, 52, 52, 16, 2, 2, 2, 9, 9, 9, 9, 9, 3, 3, 7, 16, 16, 16, 16, 52, 99, 99, 122, 122, 16, 16] 201 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 498 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113524 none CN1N=C(C2CC2)N=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 52, 52, 119, 119, 52, 52, 20, 20, 20, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 52, 52, 52, 119, 119, 119, 119, 119, 52, 52, 20, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [44, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 434 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113524 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113524/1 /scratch/stefan/7770410/working/building/REAL300020113524 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 654) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/654 `/scratch/stefan/7770410/working/3D/654' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C2CC2)N=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113524.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113524 none CN1N=C(C2CC2)N=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 9, 9, 9, 16, 29, 29, 29, 52, 52, 52, 119, 119, 119, 179, 201, 201, 201, 201, 201, 119, 119, 52, 9, 9, 9, 1, 1, 1, 1, 1, 16, 16, 29, 52, 52, 52, 52, 119, 179, 179, 201, 201, 52, 52] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 35, 36] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 723 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113524 none CN1N=C(C2CC2)N=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 120, 120, 120, 201, 201, 120, 120, 50, 50, 50, 32, 32, 32, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 32, 120, 120, 120, 201, 201, 201, 201, 201, 120, 120, 50, 32, 32, 32, 32, 7, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 785 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113524 none CN1N=C(C2CC2)N=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 52, 52, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 20, 32, 32, 32, 32, 32, 7, 7, 1, 16, 16, 16, 52, 52, 52, 52, 52, 16, 16, 5, 1, 1, 1, 1, 7, 20, 20, 32, 32, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 16, 49, 50, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 292 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113524 none CN1N=C(C2CC2)N=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 1, 1, 1, 3, 7, 7, 7, 16, 16, 16, 53, 53, 53, 101, 124, 124, 124, 124, 124, 53, 53, 16, 2, 2, 2, 9, 9, 9, 9, 9, 3, 3, 7, 16, 16, 16, 16, 53, 101, 101, 124, 124, 16, 16] 201 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 502 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113524 none CN1N=C(C2CC2)N=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 119, 119, 53, 53, 21, 21, 21, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 53, 53, 53, 119, 119, 119, 119, 119, 53, 53, 21, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [44, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 432 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113524 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113524 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113524/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113524/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113524 Building REAL300020113525 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113525' /scratch/stefan/7770410/working/building/REAL300020113525 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for REAL300020113525 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113525/0 /scratch/stefan/7770410/working/building/REAL300020113525 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/655 `/scratch/stefan/7770410/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1) `REAL300020113525.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113525 none CCN1CCOC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 20, 20, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 34, 51, 60, 60, 60, 60, 11, 11, 1, 20, 29, 29, 29, 29, 29, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 11, 34, 34, 51, 51, 1, 1, 20, 20] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50]) total number of confs: 332 number of broken/clashed sets: 71 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113525 none CCN1CCOC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 80, 80, 80, 80, 80, 40, 40, 40, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 80, 110, 110, 110, 110, 110, 80, 80, 80, 80, 80, 40, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 80, 80] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 441 number of broken/clashed sets: 71 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113525 none CCN1CCOC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 80, 80, 80, 160, 191, 201, 201, 201, 201, 80, 80, 20, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 6, 20, 20, 20, 20, 80, 160, 160, 191, 191, 20, 20, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 49, 50, 35, 36, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 701 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113525 none CCN1CCOC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 137, 137, 137, 61, 61, 61, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 61, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 137, 61, 61, 61, 61, 10, 6, 6, 4, 4, 61, 61, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 607 number of broken/clashed sets: 71 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113525 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113525/1 /scratch/stefan/7770410/working/building/REAL300020113525 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 656) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/656 `/scratch/stefan/7770410/working/3D/656' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1) `REAL300020113525.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113525/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113525 none CCN1CCOC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 20, 20, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 34, 51, 60, 60, 60, 60, 11, 11, 1, 20, 30, 30, 30, 30, 30, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 11, 34, 34, 51, 51, 1, 1, 20, 20] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50]) total number of confs: 338 number of broken/clashed sets: 72 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113525 none CCN1CCOC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 80, 80, 80, 80, 80, 40, 40, 40, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 80, 110, 110, 110, 110, 110, 80, 80, 80, 80, 80, 40, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 80, 80] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 441 number of broken/clashed sets: 72 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113525 none CCN1CCOC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 80, 80, 80, 160, 191, 201, 201, 201, 201, 80, 80, 20, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 6, 20, 20, 20, 20, 80, 160, 160, 191, 191, 20, 20, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 49, 50, 35, 36, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 701 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113525 none CCN1CCOC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 137, 137, 137, 61, 61, 61, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 61, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 137, 61, 61, 61, 61, 10, 6, 6, 4, 4, 61, 61, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 607 number of broken/clashed sets: 71 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113525 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `2' /scratch/stefan/7770410/working/building/REAL300020113525/2 /scratch/stefan/7770410/working/building/REAL300020113525 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 2 (index: 657) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/657 `/scratch/stefan/7770410/working/3D/657' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+]1CCOC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1) `REAL300020113525.mol2' -> `2.mol2' `temp.mol2' -> `REAL300020113525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113525/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113525 none CC[N@@H+]1CCOC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 9, 9, 9, 9, 9, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 9, 13, 13, 13, 13, 13, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 9, 9] 23 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50, 51]) total number of confs: 55 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113525 none CC[N@@H+]1CCOC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 13, 13, 13, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 13, 8, 8, 8, 8, 1, 3, 3, 3, 3, 8, 8, 23, 23] 23 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 78 number of broken/clashed sets: 22 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113525 none CC[N@@H+]1CCOC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 7, 9, 9, 9, 9, 23, 23, 23, 23, 23, 9, 9, 1, 1] 23 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 8, 7, 34, 50, 35, 36, 27, 51, 37] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 51 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113525 none CC[N@@H+]1CCOC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 13, 13, 13, 8, 8, 8, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 13, 8, 8, 8, 8, 3, 3, 3, 1, 1, 8, 8, 22, 22] 22 rigid atoms, others: [46, 47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 74 number of broken/clashed sets: 21 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113525 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `3' /scratch/stefan/7770410/working/building/REAL300020113525/3 /scratch/stefan/7770410/working/building/REAL300020113525 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 3 (index: 658) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/658 `/scratch/stefan/7770410/working/3D/658' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+]1CCOC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1) `REAL300020113525.mol2' -> `3.mol2' `temp.mol2' -> `REAL300020113525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113525/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113525 none CC[N@H+]1CCOC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [16, 11, 11, 11, 11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 11, 16, 16, 16, 16, 16, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 11, 11] 34 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50, 51]) total number of confs: 68 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113525 none CC[N@H+]1CCOC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 21, 21, 21, 9, 9, 9, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 9, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 21, 9, 9, 9, 9, 1, 3, 3, 3, 3, 9, 9, 34, 34] 34 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 106 number of broken/clashed sets: 33 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113525 none CC[N@H+]1CCOC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 11, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 6, 11, 11, 11, 11, 34, 34, 34, 34, 34, 11, 11, 1, 1] 34 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 8, 7, 34, 50, 35, 36, 27, 51, 37] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 69 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113525 none CC[N@H+]1CCOC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 21, 21, 21, 9, 9, 9, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 21, 9, 9, 9, 9, 3, 3, 3, 1, 1, 9, 9, 32, 32] 32 rigid atoms, others: [46, 47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 96 number of broken/clashed sets: 31 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113525 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113525 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 2: /scratch/stefan/7770410/working/building/REAL300020113525/2.* 1: /scratch/stefan/7770410/working/building/REAL300020113525/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113525/0.* 3: /scratch/stefan/7770410/working/building/REAL300020113525/3.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113525 Building REAL300020113526 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113526' /scratch/stefan/7770410/working/building/REAL300020113526 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113526 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113526/0 /scratch/stefan/7770410/working/building/REAL300020113526 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 659) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/659 `/scratch/stefan/7770410/working/3D/659' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCOC1=CC=CN=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113526.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113526 none O=C(CCCOC1=CC=CN=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 16, 16, 16, 33, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 7, 7, 7, 20, 32, 32, 32, 32, 32, 7, 7, 1, 16, 16, 16, 16, 16, 16, 43, 43, 43, 43, 5, 1, 1, 1, 1, 7, 20, 20, 32, 32, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 16, 49, 50, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 238 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113526 none O=C(CCCOC1=CC=CN=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 53, 53, 53, 104, 125, 125, 125, 125, 125, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 53, 53, 53, 53, 53, 53, 125, 125, 125, 125, 20, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [44, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 352 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113526 none O=C(CCCOC1=CC=CN=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 13, 13, 10, 6, 1, 1, 1, 1, 1, 1, 1, 27, 27, 43, 43, 43, 125, 125, 125, 173, 201, 201, 201, 201, 201, 125, 125, 43, 13, 13, 13, 13, 10, 10, 1, 1, 1, 1, 27, 43, 43, 43, 43, 125, 173, 173, 201, 201, 43, 43] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 691 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113526 none O=C(CCCOC1=CC=CN=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 119, 117, 119, 179, 201, 201, 201, 201, 201, 32, 32, 32, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 32, 119, 119, 119, 119, 118, 118, 201, 201, 201, 201, 67, 32, 32, 32, 32, 7, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 616 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113526 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113526/1 /scratch/stefan/7770410/working/building/REAL300020113526 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 660) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/660 `/scratch/stefan/7770410/working/3D/660' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCOC1=CC=CN=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113526.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113526/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113526 none O=C(CCCOC1=CC=CN=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 17, 17, 17, 34, 44, 44, 44, 44, 44, 1, 1, 1, 1, 1, 7, 7, 7, 20, 32, 32, 32, 32, 32, 7, 7, 1, 17, 17, 17, 17, 17, 17, 44, 44, 44, 44, 5, 1, 1, 1, 1, 7, 20, 20, 32, 32, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 16, 49, 50, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 241 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113526 none O=C(CCCOC1=CC=CN=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 54, 54, 54, 105, 126, 126, 126, 126, 126, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 54, 54, 54, 54, 54, 54, 126, 126, 126, 126, 20, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [44, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 358 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113526 none O=C(CCCOC1=CC=CN=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 13, 13, 10, 6, 1, 1, 1, 1, 1, 1, 1, 27, 27, 44, 44, 44, 126, 126, 126, 174, 201, 201, 201, 201, 201, 126, 126, 44, 13, 13, 13, 13, 10, 10, 1, 1, 1, 1, 27, 44, 44, 44, 44, 126, 174, 174, 201, 201, 44, 44] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 687 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113526 none O=C(CCCOC1=CC=CN=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 118, 116, 118, 179, 201, 201, 201, 201, 201, 32, 32, 32, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 32, 118, 118, 118, 118, 117, 117, 201, 201, 201, 201, 66, 32, 32, 32, 32, 7, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 616 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113526 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113526 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113526/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113526/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113526 Building REAL300020113527 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113527' /scratch/stefan/7770410/working/building/REAL300020113527 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113527 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113527/0 /scratch/stefan/7770410/working/building/REAL300020113527 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/661 `/scratch/stefan/7770410/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1) `REAL300020113527.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113527 none CC1CCC(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 24, 22, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 30, 44, 47, 47, 47, 47, 10, 10, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 24, 24, 22, 22, 6, 1, 1, 1, 1, 10, 30, 30, 44, 44, 1, 1] 201 rigid atoms, others: [43, 9, 10, 11, 12, 13, 44, 50, 51, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 293 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113527 none CC1CCC(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 102, 91, 88, 27, 27, 27, 10, 10, 10, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 10, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 91, 91, 88, 88, 27, 10, 10, 10, 10, 1, 7, 7, 9, 9, 10, 10] 201 rigid atoms, others: [12, 45, 14, 13, 16, 23, 24, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 407 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113527 none CC1CCC(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 5, 14, 14, 14, 30, 30, 30, 102, 102, 102, 164, 201, 201, 201, 201, 201, 102, 102, 30, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 14, 30, 30, 30, 30, 102, 164, 164, 201, 201, 30, 30] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 35, 26, 5, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 729 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113527 none CC1CCC(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 198, 89, 89, 89, 47, 47, 47, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 47, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 198, 198, 89, 47, 47, 47, 47, 11, 6, 6, 4, 4, 47, 47] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 744 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113527 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113527/1 /scratch/stefan/7770410/working/building/REAL300020113527 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 662) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/662 `/scratch/stefan/7770410/working/3D/662' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1) `REAL300020113527.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113527 none CC1CCC(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 24, 22, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 30, 44, 47, 47, 47, 47, 10, 10, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 24, 24, 22, 22, 6, 1, 1, 1, 1, 10, 30, 30, 44, 44, 1, 1] 201 rigid atoms, others: [43, 9, 10, 11, 12, 13, 44, 50, 51, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 293 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113527 none CC1CCC(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 102, 91, 88, 28, 28, 28, 10, 10, 10, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 10, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 91, 91, 88, 88, 28, 10, 10, 10, 10, 1, 7, 7, 9, 9, 10, 10] 201 rigid atoms, others: [12, 45, 14, 13, 16, 23, 24, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 406 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113527 none CC1CCC(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 5, 14, 14, 14, 30, 30, 30, 102, 102, 102, 164, 201, 201, 201, 201, 201, 102, 102, 30, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 14, 30, 30, 30, 30, 102, 164, 164, 201, 201, 30, 30] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 35, 26, 5, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 729 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113527 none CC1CCC(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 198, 89, 89, 89, 47, 47, 47, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 47, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 198, 198, 89, 47, 47, 47, 47, 11, 6, 6, 4, 4, 47, 47] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 744 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113527 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113527 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113527/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113527/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113527 Building REAL300020113528 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113528' /scratch/stefan/7770410/working/building/REAL300020113528 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113528 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113528/0 /scratch/stefan/7770410/working/building/REAL300020113528 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/663 `/scratch/stefan/7770410/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(=O)NC(C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113528.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113528 none CC1=CC(=O)NC(C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 35, 51, 59, 59, 59, 59, 12, 12, 1, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 12, 35, 35, 51, 51, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 252 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113528 none CC1=CC(=O)NC(C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 85, 85, 85, 85, 85, 41, 41, 41, 12, 12, 12, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 12, 85, 85, 85, 85, 85, 85, 85, 85, 41, 12, 12, 12, 12, 1, 6, 6, 8, 8, 12, 12] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 218 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113528 none CC1=CC(=O)NC(C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 17, 85, 85, 85, 151, 201, 201, 201, 201, 201, 85, 85, 17, 2, 2, 2, 1, 1, 2, 2, 2, 7, 17, 17, 17, 17, 85, 151, 151, 201, 201, 17, 17] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 776 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113528 none CC1=CC(=O)NC(C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 109, 109, 109, 61, 61, 61, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 61, 201, 201, 201, 201, 201, 201, 201, 201, 109, 61, 61, 61, 61, 12, 6, 6, 4, 4, 61, 61] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 486 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113528 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113528/1 /scratch/stefan/7770410/working/building/REAL300020113528 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 664) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/664 `/scratch/stefan/7770410/working/3D/664' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(=O)NC(C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113528.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113528/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113528 none CC1=CC(=O)NC(C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 34, 50, 58, 58, 58, 58, 12, 12, 1, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 12, 34, 34, 50, 50, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 248 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113528 none CC1=CC(=O)NC(C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 84, 84, 84, 84, 84, 41, 41, 41, 12, 12, 12, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 12, 84, 84, 84, 84, 84, 84, 84, 84, 41, 12, 12, 12, 12, 1, 6, 6, 8, 8, 12, 12] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 217 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113528 none CC1=CC(=O)NC(C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 84, 84, 84, 149, 201, 201, 201, 201, 201, 84, 84, 16, 2, 2, 2, 1, 1, 2, 2, 2, 6, 16, 16, 16, 16, 84, 149, 149, 201, 201, 16, 16] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 786 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113528 none CC1=CC(=O)NC(C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 106, 106, 106, 58, 58, 58, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 58, 201, 201, 201, 201, 201, 201, 201, 201, 106, 58, 58, 58, 58, 10, 6, 6, 4, 4, 58, 58] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 488 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113528 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113528 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113528/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113528/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113528 Building REAL300020113529 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113529' /scratch/stefan/7770410/working/building/REAL300020113529 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113529 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113529/0 /scratch/stefan/7770410/working/building/REAL300020113529 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/665 `/scratch/stefan/7770410/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113529.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113529 none C[C@@H](CC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 6, 23, 23, 32, 32, 32, 32, 32, 32, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 33, 47, 47, 47, 47, 47, 13, 13, 1, 23, 23, 23, 32, 32, 32, 32, 32, 32, 32, 6, 1, 1, 1, 1, 13, 33, 33, 47, 47, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 16, 49, 50, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 314 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113529 none C[C@@H](CC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 50, 120, 120, 140, 140, 140, 140, 140, 140, 50, 50, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 120, 120, 120, 140, 140, 140, 140, 140, 140, 140, 50, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [44, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 602 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113529 none C[C@@H](CC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 1, 4, 12, 12, 12, 32, 32, 32, 140, 140, 140, 180, 201, 201, 201, 201, 201, 140, 140, 32, 4, 4, 4, 2, 2, 1, 1, 1, 1, 1, 12, 32, 32, 32, 32, 140, 180, 180, 201, 201, 32, 32] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 35, 36, 38, 37] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 558 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113529 none C[C@@H](CC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [188, 118, 188, 188, 201, 201, 201, 201, 201, 201, 118, 118, 48, 48, 48, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 48, 188, 188, 188, 201, 201, 201, 201, 201, 201, 201, 118, 48, 48, 48, 48, 9, 4, 4, 2, 2, 48, 48] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 755 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113529 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113529/1 /scratch/stefan/7770410/working/building/REAL300020113529 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 666) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/666 `/scratch/stefan/7770410/working/3D/666' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113529.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113529/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113529 none C[C@@H](CC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 6, 24, 24, 33, 33, 33, 33, 33, 33, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 33, 47, 47, 47, 47, 47, 13, 13, 1, 24, 24, 24, 33, 33, 33, 33, 33, 33, 33, 6, 1, 1, 1, 1, 13, 33, 33, 47, 47, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 16, 49, 50, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 317 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113529 none C[C@@H](CC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [121, 50, 121, 121, 141, 141, 141, 141, 141, 141, 50, 50, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 121, 121, 121, 141, 141, 141, 141, 141, 141, 141, 50, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [44, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 605 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113529 none C[C@@H](CC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 1, 4, 12, 12, 12, 33, 33, 33, 141, 141, 141, 179, 201, 201, 201, 201, 201, 141, 141, 33, 4, 4, 4, 2, 2, 1, 1, 1, 1, 1, 12, 33, 33, 33, 33, 141, 179, 179, 201, 201, 33, 33] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 35, 36, 38, 37] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 557 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113529 none C[C@@H](CC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [188, 119, 188, 188, 201, 201, 201, 201, 201, 201, 119, 119, 49, 49, 49, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 49, 188, 188, 188, 201, 201, 201, 201, 201, 201, 201, 119, 49, 49, 49, 49, 9, 4, 4, 2, 2, 49, 49] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 754 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113529 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113529 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113529/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113529/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113529 Building REAL300020113530 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113530' /scratch/stefan/7770410/working/building/REAL300020113530 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113530 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113530/0 /scratch/stefan/7770410/working/building/REAL300020113530 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 667) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/667 `/scratch/stefan/7770410/working/3D/667' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113530.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113530 none C[C@H](CC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 16, 16, 26, 26, 26, 26, 26, 26, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 32, 46, 49, 49, 49, 49, 10, 10, 1, 16, 16, 16, 26, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 10, 32, 32, 46, 46, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 16, 49, 50, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 305 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113530 none C[C@H](CC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 34, 73, 73, 112, 112, 112, 112, 112, 112, 34, 34, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 10, 73, 73, 73, 112, 112, 112, 112, 112, 112, 112, 34, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10] 201 rigid atoms, others: [44, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 515 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113530 none C[C@H](CC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 1, 4, 10, 10, 10, 26, 26, 26, 112, 112, 112, 171, 201, 201, 201, 201, 201, 112, 112, 26, 4, 4, 4, 2, 2, 1, 1, 1, 1, 1, 10, 26, 26, 26, 26, 112, 171, 171, 201, 201, 26, 26] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 35, 36, 38, 37] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 687 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113530 none C[C@H](CC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [174, 103, 174, 174, 201, 201, 201, 201, 201, 201, 103, 103, 51, 51, 51, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 51, 174, 174, 174, 201, 201, 201, 201, 201, 201, 201, 103, 51, 51, 51, 51, 11, 6, 6, 4, 4, 51, 51] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 788 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113530 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113530/1 /scratch/stefan/7770410/working/building/REAL300020113530 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 668) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/668 `/scratch/stefan/7770410/working/3D/668' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113530.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113530 none C[C@H](CC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 16, 16, 26, 26, 26, 26, 26, 26, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 32, 46, 49, 49, 49, 49, 10, 10, 1, 16, 16, 16, 26, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 10, 32, 32, 46, 46, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 16, 49, 50, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 305 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113530 none C[C@H](CC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 34, 73, 73, 112, 112, 112, 112, 112, 112, 34, 34, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 10, 73, 73, 73, 112, 112, 112, 112, 112, 112, 112, 34, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10] 201 rigid atoms, others: [44, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 515 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113530 none C[C@H](CC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 1, 4, 10, 10, 10, 26, 26, 26, 112, 112, 112, 171, 201, 201, 201, 201, 201, 112, 112, 26, 4, 4, 4, 2, 2, 1, 1, 1, 1, 1, 10, 26, 26, 26, 26, 112, 171, 171, 201, 201, 26, 26] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 35, 36, 38, 37] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 687 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113530 none C[C@H](CC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [174, 103, 174, 174, 201, 201, 201, 201, 201, 201, 103, 103, 50, 50, 50, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 50, 174, 174, 174, 201, 201, 201, 201, 201, 201, 201, 103, 50, 50, 50, 50, 11, 6, 6, 4, 4, 50, 50] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 790 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113530 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113530 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113530/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113530/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113530 Building REAL300020113531 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113531' /scratch/stefan/7770410/working/building/REAL300020113531 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113531 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113531/0 /scratch/stefan/7770410/working/building/REAL300020113531 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/669 `/scratch/stefan/7770410/working/3D/669' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1) `REAL300020113531.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113531 none C=CCC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 76, 48, 27, 27, 27, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 8, 48, 52, 52, 48, 52, 52, 115, 115, 115, 76, 76, 48, 27, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8, 52, 52, 52, 52, 52] 201 rigid atoms, others: [40, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 552 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113531 none C=CCC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 191, 131, 80, 80, 80, 34, 34, 34, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 10, 10, 34, 131, 141, 141, 131, 141, 141, 201, 201, 201, 191, 191, 131, 80, 34, 34, 34, 34, 10, 4, 4, 4, 4, 34, 34, 141, 141, 141, 141, 141] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 947 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113531 none C=CCC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 20, 12, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 24, 37, 40, 40, 40, 40, 8, 8, 1, 12, 14, 14, 12, 14, 14, 36, 36, 36, 20, 20, 12, 6, 1, 1, 1, 1, 8, 24, 24, 37, 37, 1, 1, 14, 14, 14, 14, 14] 201 rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 39, 45, 46, 22, 38] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113531 none C=CCC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 3, 1, 3, 6, 6, 6, 14, 14, 14, 52, 52, 52, 105, 135, 138, 138, 138, 138, 52, 52, 14, 1, 1, 1, 1, 1, 1, 11, 11, 11, 5, 5, 3, 6, 14, 14, 14, 14, 52, 105, 105, 135, 135, 14, 14, 1, 1, 1, 1, 1] 201 rigid atoms, others: [3, 47, 48, 49, 50, 51, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 557 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113531 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113531/1 /scratch/stefan/7770410/working/building/REAL300020113531 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 670) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/670 `/scratch/stefan/7770410/working/3D/670' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1) `REAL300020113531.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113531/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113531 none C=CCC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 76, 48, 27, 27, 27, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 8, 48, 52, 52, 48, 52, 52, 115, 115, 115, 76, 76, 48, 27, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8, 52, 52, 52, 52, 52] 201 rigid atoms, others: [40, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 552 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113531 none C=CCC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 191, 131, 80, 80, 80, 34, 34, 34, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 9, 9, 34, 131, 141, 141, 131, 141, 141, 201, 201, 201, 191, 191, 131, 80, 34, 34, 34, 34, 9, 4, 4, 4, 4, 34, 34, 141, 141, 141, 141, 141] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 948 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113531 none C=CCC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 20, 12, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 24, 37, 40, 40, 40, 40, 8, 8, 1, 12, 14, 14, 12, 14, 14, 36, 36, 36, 20, 20, 12, 6, 1, 1, 1, 1, 8, 24, 24, 37, 37, 1, 1, 14, 14, 14, 14, 14] 201 rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 39, 45, 46, 22, 38] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113531 none C=CCC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 3, 1, 3, 6, 6, 6, 14, 14, 14, 52, 52, 52, 105, 135, 138, 138, 138, 138, 52, 52, 14, 1, 1, 1, 1, 1, 1, 11, 11, 11, 5, 5, 3, 6, 14, 14, 14, 14, 52, 105, 105, 135, 135, 14, 14, 1, 1, 1, 1, 1] 201 rigid atoms, others: [3, 47, 48, 49, 50, 51, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 557 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113531 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113531 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113531/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113531/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113531 Building REAL300020113532 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113532' /scratch/stefan/7770410/working/building/REAL300020113532 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113532 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113532/0 /scratch/stefan/7770410/working/building/REAL300020113532 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 671) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/671 `/scratch/stefan/7770410/working/3D/671' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C12CCC(CC1)CC2) `REAL300020113532.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113532 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C12CCC(CC1)CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 13, 13, 13, 1, 1, 1, 1, 1, 8, 12, 18, 18, 18, 18, 1, 1, 13, 55, 84, 84, 55, 84, 84, 84, 84, 55, 13, 13, 13, 13, 1, 8, 8, 12, 12, 13, 13, 84, 84, 84, 84, 55, 84, 84, 84, 84, 84, 84, 84, 84] 199 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 392 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113532 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C12CCC(CC1)CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [176, 176, 113, 113, 113, 19, 19, 19, 6, 4, 1, 1, 1, 1, 1, 1, 19, 19, 113, 176, 197, 197, 176, 197, 197, 197, 197, 176, 113, 113, 113, 113, 19, 6, 6, 4, 4, 113, 113, 197, 197, 197, 197, 176, 197, 197, 197, 197, 197, 197, 197, 197] 197 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 642 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113532 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C12CCC(CC1)CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 62, 86, 113, 113, 113, 113, 13, 13, 1, 6, 12, 12, 6, 12, 12, 12, 12, 6, 1, 1, 1, 1, 13, 62, 62, 86, 86, 1, 1, 12, 12, 12, 12, 6, 12, 12, 12, 12, 12, 12, 12, 12] 199 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 445 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113532 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C12CCC(CC1)CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 12, 12, 12, 84, 84, 84, 170, 199, 199, 199, 199, 199, 84, 84, 12, 1, 1, 1, 1, 1, 1, 1, 1, 4, 12, 12, 12, 12, 84, 170, 170, 199, 199, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 199 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 714 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113532 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113532/1 /scratch/stefan/7770410/working/building/REAL300020113532 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 672) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/672 `/scratch/stefan/7770410/working/3D/672' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C12CCC(CC1)CC2) `REAL300020113532.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113532/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113532 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C12CCC(CC1)CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 13, 13, 13, 1, 1, 1, 1, 1, 8, 12, 18, 18, 18, 18, 1, 1, 13, 55, 84, 84, 55, 84, 84, 84, 84, 55, 13, 13, 13, 13, 1, 8, 8, 12, 12, 13, 13, 84, 84, 84, 84, 55, 84, 84, 84, 84, 84, 84, 84, 84] 198 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 392 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113532 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C12CCC(CC1)CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [176, 176, 113, 113, 113, 19, 19, 19, 6, 4, 1, 1, 1, 1, 1, 1, 19, 19, 113, 176, 197, 197, 176, 197, 197, 197, 197, 176, 113, 113, 113, 113, 19, 6, 6, 4, 4, 113, 113, 197, 197, 197, 197, 176, 197, 197, 197, 197, 197, 197, 197, 197] 197 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 642 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113532 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C12CCC(CC1)CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 62, 86, 113, 113, 113, 113, 13, 13, 1, 6, 13, 13, 6, 13, 13, 13, 13, 6, 1, 1, 1, 1, 13, 62, 62, 86, 86, 1, 1, 13, 13, 13, 13, 6, 13, 13, 13, 13, 13, 13, 13, 13] 198 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 448 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113532 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C12CCC(CC1)CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 13, 13, 13, 84, 84, 84, 169, 198, 198, 198, 198, 198, 84, 84, 13, 1, 1, 1, 1, 1, 1, 1, 1, 4, 13, 13, 13, 13, 84, 169, 169, 198, 198, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 198 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 708 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113532 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113532 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113532/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113532/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113532 Building REAL300020113533 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113533' /scratch/stefan/7770410/working/building/REAL300020113533 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113533 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113533/0 /scratch/stefan/7770410/working/building/REAL300020113533 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/673 `/scratch/stefan/7770410/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(C)(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113533.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113533 none CCCCCC(C)(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 87, 87, 73, 39, 73, 73, 39, 39, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 89, 89, 89, 89, 89, 89, 89, 87, 87, 87, 87, 73, 73, 73, 73, 73, 73, 39, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11] 201 rigid atoms, others: [17, 13, 14, 15, 16, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55]) total number of confs: 423 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113533 none CCCCCC(C)(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 199, 199, 193, 130, 193, 193, 130, 130, 59, 59, 59, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 59, 201, 201, 201, 201, 201, 201, 201, 199, 199, 199, 199, 193, 193, 193, 193, 193, 193, 130, 59, 59, 59, 59, 12, 6, 6, 4, 4, 59, 59] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 771 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113533 none CCCCCC(C)(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 23, 23, 13, 6, 13, 13, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 37, 50, 59, 59, 59, 59, 11, 11, 1, 25, 25, 25, 25, 25, 25, 25, 23, 23, 23, 23, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 11, 37, 37, 50, 50, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 46, 45, 48, 14, 54, 55, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53]) total number of confs: 321 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113533 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113533/1 /scratch/stefan/7770410/working/building/REAL300020113533 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 674) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/674 `/scratch/stefan/7770410/working/3D/674' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(C)(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113533.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113533 none CCCCCC(C)(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 87, 87, 73, 39, 73, 73, 39, 39, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 89, 89, 89, 89, 89, 89, 89, 87, 87, 87, 87, 73, 73, 73, 73, 73, 73, 39, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11] 201 rigid atoms, others: [17, 13, 14, 15, 16, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55]) total number of confs: 423 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113533 none CCCCCC(C)(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 199, 199, 193, 130, 193, 193, 130, 130, 59, 59, 59, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 59, 201, 201, 201, 201, 201, 201, 201, 199, 199, 199, 199, 193, 193, 193, 193, 193, 193, 130, 59, 59, 59, 59, 12, 6, 6, 4, 4, 59, 59] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 771 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113533 none CCCCCC(C)(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 23, 23, 13, 6, 13, 13, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 37, 50, 59, 59, 59, 59, 11, 11, 1, 25, 25, 25, 25, 25, 25, 25, 23, 23, 23, 23, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 11, 37, 37, 50, 50, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 46, 45, 48, 14, 54, 55, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53]) total number of confs: 321 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113533 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113533 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113533/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113533/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113533 Building REAL300020113534 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113534' /scratch/stefan/7770410/working/building/REAL300020113534 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113534 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113534/0 /scratch/stefan/7770410/working/building/REAL300020113534 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 675) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/675 `/scratch/stefan/7770410/working/3D/675' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H](NC(C)=O)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113534.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113534 none CC[C@H](C)[C@H](NC(C)=O)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 5, 6, 6, 4, 5, 5, 5, 5, 5, 4, 4, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 3, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 4, 3, 3, 3, 3, 1, 3, 3, 3, 3, 3, 3] 6 rigid atoms, others: [47, 16, 17, 18, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 32 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113534 none CC[C@H](C)[C@H](NC(C)=O)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 5, 6, 6, 4, 5, 5, 5, 5, 5, 4, 4, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 4, 3, 3, 3, 3, 3, 3, 3, 1, 1, 3, 3] 6 rigid atoms, others: [50, 51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 26 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113534 none CC[C@H](C)[C@H](NC(C)=O)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 5, 6, 6, 4, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 4, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1] 6 rigid atoms, others: [45, 43, 44, 13, 14, 15, 16, 17, 52, 46, 29, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 24 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113534 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113534/1 /scratch/stefan/7770410/working/building/REAL300020113534 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 676) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/676 `/scratch/stefan/7770410/working/3D/676' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H](NC(C)=O)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113534.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113534 none CC[C@H](C)[C@H](NC(C)=O)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 5, 6, 6, 4, 5, 5, 5, 5, 5, 4, 4, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 3, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 4, 3, 3, 3, 3, 1, 3, 3, 3, 3, 3, 3] 6 rigid atoms, others: [47, 16, 17, 18, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 32 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113534 none CC[C@H](C)[C@H](NC(C)=O)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 5, 6, 6, 4, 5, 5, 5, 5, 5, 4, 4, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 4, 3, 3, 3, 3, 3, 3, 3, 1, 1, 3, 3] 6 rigid atoms, others: [50, 51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 26 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113534 none CC[C@H](C)[C@H](NC(C)=O)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 5, 6, 6, 4, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 4, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1] 6 rigid atoms, others: [45, 43, 44, 13, 14, 15, 16, 17, 52, 46, 29, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 24 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113534 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113534 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113534/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113534/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113534 Building REAL300020113535 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113535' /scratch/stefan/7770410/working/building/REAL300020113535 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113535 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113535/0 /scratch/stefan/7770410/working/building/REAL300020113535 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/677 `/scratch/stefan/7770410/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(CC)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113535.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113535 none CCCCCC(CC)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 103, 61, 33, 61, 61, 33, 33, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 10, 103, 103, 103, 103, 103, 103, 103, 103, 103, 103, 103, 61, 61, 61, 61, 61, 61, 33, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10] 201 rigid atoms, others: [17, 13, 14, 15, 16, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55]) total number of confs: 472 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113535 none CCCCCC(CC)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 153, 103, 153, 152, 103, 103, 43, 43, 43, 11, 11, 11, 4, 4, 1, 1, 1, 1, 1, 1, 11, 11, 43, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 153, 153, 153, 153, 153, 153, 103, 43, 43, 43, 43, 11, 4, 4, 4, 4, 43, 43] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 828 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113535 none CCCCCC(CC)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 13, 6, 13, 13, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 28, 41, 45, 45, 45, 45, 10, 10, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 10, 28, 28, 41, 41, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 46, 45, 48, 14, 54, 55, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53]) total number of confs: 283 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113535 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113535/1 /scratch/stefan/7770410/working/building/REAL300020113535 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 678) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/678 `/scratch/stefan/7770410/working/3D/678' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(CC)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113535.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113535/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113535 none CCCCCC(CC)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 104, 62, 33, 62, 62, 33, 33, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 10, 104, 104, 104, 104, 104, 104, 104, 104, 104, 104, 104, 62, 62, 62, 62, 62, 62, 33, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10] 201 rigid atoms, others: [17, 13, 14, 15, 16, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55]) total number of confs: 475 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113535 none CCCCCC(CC)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 152, 102, 152, 151, 102, 102, 42, 42, 42, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 10, 10, 42, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 152, 152, 152, 152, 152, 152, 102, 42, 42, 42, 42, 10, 4, 4, 4, 4, 42, 42] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 831 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113535 none CCCCCC(CC)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 28, 41, 45, 45, 45, 45, 10, 10, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 10, 28, 28, 41, 41, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 46, 45, 48, 14, 54, 55, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113535 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113535 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113535/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113535/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113535 Building REAL300020113536 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113536' /scratch/stefan/7770410/working/building/REAL300020113536 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113536 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113536/0 /scratch/stefan/7770410/working/building/REAL300020113536 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/679 `/scratch/stefan/7770410/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(C2CC2)C=C1) `REAL300020113536.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113536 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(C2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 7, 28, 47, 47, 28, 28, 88, 88, 47, 47, 28, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7, 47, 47, 88, 88, 88, 88, 88, 47, 47] 187 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 377 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113536 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(C2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 8, 26, 26, 26, 88, 88, 88, 170, 187, 187, 187, 187, 187, 88, 88, 26, 4, 6, 6, 1, 1, 1, 1, 6, 6, 8, 26, 26, 26, 26, 88, 170, 170, 187, 187, 26, 26, 6, 6, 1, 1, 1, 1, 1, 6, 6] 187 rigid atoms, others: [42, 43, 44, 45, 46, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48]) total number of confs: 645 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113536 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(C2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [124, 124, 65, 65, 65, 21, 21, 21, 6, 4, 1, 1, 1, 1, 1, 1, 21, 21, 65, 124, 165, 165, 124, 124, 187, 187, 165, 165, 124, 65, 65, 65, 65, 21, 6, 6, 4, 4, 65, 65, 165, 165, 187, 187, 187, 187, 187, 165, 165] 187 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 768 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113536 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(C2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 38, 46, 59, 59, 59, 59, 7, 7, 1, 6, 11, 11, 6, 6, 26, 26, 11, 11, 6, 1, 1, 1, 1, 7, 38, 38, 46, 46, 1, 1, 11, 11, 26, 26, 26, 26, 26, 11, 11] 187 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 280 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113536 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(C2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 11, 11, 11, 47, 47, 47, 126, 153, 164, 164, 164, 164, 47, 47, 11, 1, 1, 1, 1, 1, 6, 6, 1, 1, 3, 11, 11, 11, 11, 47, 126, 126, 153, 153, 11, 11, 1, 1, 6, 6, 6, 6, 6, 1, 1] 187 rigid atoms, others: [1, 40, 41, 47, 48, 19, 20, 21, 22, 23, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46]) total number of confs: 596 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113536 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113536/1 /scratch/stefan/7770410/working/building/REAL300020113536 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 680) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/680 `/scratch/stefan/7770410/working/3D/680' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(C2CC2)C=C1) `REAL300020113536.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113536/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113536 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(C2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 7, 28, 47, 47, 28, 28, 88, 88, 47, 47, 28, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7, 47, 47, 88, 88, 88, 88, 88, 47, 47] 187 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 377 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113536 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(C2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 8, 26, 26, 26, 88, 88, 88, 170, 187, 187, 187, 187, 187, 88, 88, 26, 4, 6, 6, 1, 1, 1, 1, 6, 6, 8, 26, 26, 26, 26, 88, 170, 170, 187, 187, 26, 26, 6, 6, 1, 1, 1, 1, 1, 6, 6] 187 rigid atoms, others: [42, 43, 44, 45, 46, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48]) total number of confs: 645 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113536 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(C2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [123, 123, 64, 64, 64, 21, 21, 21, 6, 4, 1, 1, 1, 1, 1, 1, 21, 21, 64, 123, 165, 165, 123, 123, 187, 187, 165, 165, 123, 64, 64, 64, 64, 21, 6, 6, 4, 4, 64, 64, 165, 165, 187, 187, 187, 187, 187, 165, 165] 187 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 775 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113536 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(C2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 38, 46, 59, 59, 59, 59, 7, 7, 1, 6, 11, 11, 6, 6, 26, 26, 11, 11, 6, 1, 1, 1, 1, 7, 38, 38, 46, 46, 1, 1, 11, 11, 26, 26, 26, 26, 26, 11, 11] 187 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 280 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113536 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(C2CC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 11, 11, 11, 47, 47, 47, 126, 153, 164, 164, 164, 164, 47, 47, 11, 1, 1, 1, 1, 1, 6, 6, 1, 1, 3, 11, 11, 11, 11, 47, 126, 126, 153, 153, 11, 11, 1, 1, 6, 6, 6, 6, 6, 1, 1] 187 rigid atoms, others: [1, 40, 41, 47, 48, 19, 20, 21, 22, 23, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46]) total number of confs: 596 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113536 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113536 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113536/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113536/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113536 Building REAL300020113537 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113537' /scratch/stefan/7770410/working/building/REAL300020113537 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113537 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113537/0 /scratch/stefan/7770410/working/building/REAL300020113537 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/681 `/scratch/stefan/7770410/working/3D/681' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CCC(C)(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1) `REAL300020113537.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113537 none CC1=CCC(C)(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 6, 9, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 43, 61, 67, 67, 67, 67, 12, 12, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 1, 1, 1, 1, 12, 43, 43, 61, 61, 1, 1, 9, 9, 9, 9] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 46, 47, 40, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 283 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113537 none CC1=CCC(C)(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 51, 63, 51, 51, 12, 12, 12, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 12, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 51, 12, 12, 12, 12, 1, 8, 8, 10, 10, 12, 12, 63, 63, 63, 63] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 213 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113537 none CC1=CCC(C)(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 63, 63, 63, 148, 201, 201, 201, 201, 201, 63, 63, 9, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 9, 9, 9, 9, 63, 148, 148, 201, 201, 9, 9, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 48, 49, 50, 51, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 808 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113537 none CC1=CCC(C)(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 182, 201, 182, 182, 67, 67, 67, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 67, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 182, 67, 67, 67, 67, 12, 6, 6, 4, 4, 67, 67, 201, 201, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 565 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113537 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113537/1 /scratch/stefan/7770410/working/building/REAL300020113537 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 682) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/682 `/scratch/stefan/7770410/working/3D/682' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CCC(C)(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1) `REAL300020113537.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113537/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113537 none CC1=CCC(C)(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 6, 9, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 43, 61, 67, 67, 67, 67, 12, 12, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 1, 1, 1, 1, 12, 43, 43, 61, 61, 1, 1, 9, 9, 9, 9] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 46, 47, 40, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 283 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113537 none CC1=CCC(C)(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 51, 63, 51, 51, 12, 12, 12, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 12, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 51, 12, 12, 12, 12, 1, 8, 8, 10, 10, 12, 12, 63, 63, 63, 63] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 213 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113537 none CC1=CCC(C)(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 63, 63, 63, 148, 201, 201, 201, 201, 201, 63, 63, 9, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 9, 9, 9, 9, 63, 148, 148, 201, 201, 9, 9, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 48, 49, 50, 51, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 808 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113537 none CC1=CCC(C)(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 182, 201, 182, 182, 67, 67, 67, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 67, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 182, 67, 67, 67, 67, 12, 6, 6, 4, 4, 67, 67, 201, 201, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 565 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113537 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113537 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113537/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113537/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113537 Building REAL300020113538 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113538' /scratch/stefan/7770410/working/building/REAL300020113538 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113538 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113538/0 /scratch/stefan/7770410/working/building/REAL300020113538 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 683) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/683 `/scratch/stefan/7770410/working/3D/683' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)CC(C)(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113538.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113538 none CC(C)(C)CC(C)(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 12, 12, 12, 1, 1, 1, 1, 1, 9, 14, 19, 19, 19, 19, 1, 1, 12, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 12, 12, 12, 12, 1, 9, 9, 14, 14, 12, 12] 142 rigid atoms, others: [17, 13, 14, 15, 16, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55]) total number of confs: 196 number of broken/clashed sets: 142 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113538 none CC(C)(C)CC(C)(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 44, 44, 44, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 44, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 44, 44, 44, 44, 13, 6, 6, 4, 4, 44, 44] 49 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 135 number of broken/clashed sets: 49 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113538 none CC(C)(C)CC(C)(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 53, 77, 92, 92, 92, 92, 12, 12, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 12, 53, 53, 77, 77, 1, 1] 142 rigid atoms, others: [10, 11, 12, 13, 46, 45, 48, 14, 54, 55, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53]) total number of confs: 355 number of broken/clashed sets: 142 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113538 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113538/1 /scratch/stefan/7770410/working/building/REAL300020113538 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 684) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/684 `/scratch/stefan/7770410/working/3D/684' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)CC(C)(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113538.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113538 none CC(C)(C)CC(C)(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 12, 12, 12, 1, 1, 1, 1, 1, 9, 14, 19, 19, 19, 19, 1, 1, 12, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 12, 12, 12, 12, 1, 9, 9, 14, 14, 12, 12] 143 rigid atoms, others: [17, 13, 14, 15, 16, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55]) total number of confs: 196 number of broken/clashed sets: 143 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113538 none CC(C)(C)CC(C)(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 44, 44, 44, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 44, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 44, 44, 44, 44, 13, 6, 6, 4, 4, 44, 44] 49 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 135 number of broken/clashed sets: 49 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113538 none CC(C)(C)CC(C)(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 54, 77, 94, 94, 94, 94, 12, 12, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 12, 54, 54, 77, 77, 1, 1] 143 rigid atoms, others: [10, 11, 12, 13, 46, 45, 48, 14, 54, 55, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53]) total number of confs: 356 number of broken/clashed sets: 143 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113538 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113538 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113538/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113538/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113538 Building REAL300020113539 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113539' /scratch/stefan/7770410/working/building/REAL300020113539 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113539 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113539/0 /scratch/stefan/7770410/working/building/REAL300020113539 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/685 `/scratch/stefan/7770410/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1) `REAL300020113539.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113539 none C=CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 98, 79, 25, 25, 25, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 98, 100, 100, 98, 100, 100, 102, 102, 102, 98, 79, 79, 25, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 100, 100, 98, 100, 100] 201 rigid atoms, others: [40, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 444 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113539 none C=CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 197, 87, 87, 87, 45, 45, 45, 11, 11, 11, 5, 3, 1, 1, 1, 1, 1, 1, 11, 11, 45, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 197, 197, 87, 45, 45, 45, 45, 11, 5, 5, 3, 3, 45, 45, 201, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 750 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113539 none C=CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 29, 21, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 29, 42, 43, 43, 43, 43, 8, 8, 1, 29, 31, 31, 29, 31, 31, 36, 36, 36, 29, 21, 21, 5, 1, 1, 1, 1, 8, 29, 29, 42, 42, 1, 1, 31, 31, 29, 31, 31] 201 rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 39, 45, 46, 22, 38] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51]) total number of confs: 322 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113539 none C=CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 1, 3, 6, 14, 14, 14, 31, 31, 31, 100, 100, 100, 164, 201, 201, 201, 201, 201, 100, 100, 31, 1, 1, 1, 1, 1, 1, 5, 5, 5, 3, 6, 6, 14, 31, 31, 31, 31, 100, 164, 164, 201, 201, 31, 31, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 47, 48, 49, 50, 51, 23, 24, 25, 26, 27, 28] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 770 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113539 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113539/1 /scratch/stefan/7770410/working/building/REAL300020113539 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 686) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/686 `/scratch/stefan/7770410/working/3D/686' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1) `REAL300020113539.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113539/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113539 none C=CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 98, 79, 25, 25, 25, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 98, 100, 100, 98, 100, 100, 102, 102, 102, 98, 79, 79, 25, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 100, 100, 98, 100, 100] 201 rigid atoms, others: [40, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 444 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113539 none C=CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 197, 86, 86, 86, 44, 44, 44, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 44, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 197, 197, 86, 44, 44, 44, 44, 10, 5, 5, 3, 3, 44, 44, 201, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 755 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113539 none C=CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 29, 21, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 29, 42, 43, 43, 43, 43, 8, 8, 1, 29, 31, 31, 29, 31, 31, 36, 36, 36, 29, 21, 21, 5, 1, 1, 1, 1, 8, 29, 29, 42, 42, 1, 1, 31, 31, 29, 31, 31] 201 rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 39, 45, 46, 22, 38] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51]) total number of confs: 322 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113539 none C=CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 1, 3, 6, 14, 14, 14, 31, 31, 31, 100, 100, 100, 163, 201, 201, 201, 201, 201, 100, 100, 31, 1, 1, 1, 1, 1, 1, 5, 5, 5, 3, 6, 6, 14, 31, 31, 31, 31, 100, 163, 163, 201, 201, 31, 31, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 47, 48, 49, 50, 51, 23, 24, 25, 26, 27, 28] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 770 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113539 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113539 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113539/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113539/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113539 Building REAL300020113540 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113540' /scratch/stefan/7770410/working/building/REAL300020113540 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113540 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113540/0 /scratch/stefan/7770410/working/building/REAL300020113540 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 687) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/687 `/scratch/stefan/7770410/working/3D/687' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1N=CC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113540.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113540 none O=C(CN1N=CC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 8, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 18, 20, 20, 20, 20, 1, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 5, 5, 5, 4, 4, 1, 18, 18, 20, 20, 6, 1, 1, 1, 1, 4, 5, 5, 5, 5, 1, 1] 25 rigid atoms, others: [32, 33, 39, 8, 9, 10, 11, 12, 40, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38]) total number of confs: 75 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113540 none O=C(CN1N=CC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 8, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 19, 21, 21, 21, 21, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 4, 19, 19, 21, 21, 9, 4, 4, 4, 4, 1, 4, 4, 4, 4, 4, 4] 25 rigid atoms, others: [34, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 78 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113540 none O=C(CN1N=CC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 8, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 13, 13, 20, 20, 20, 21, 21, 21, 25, 25, 25, 25, 25, 25, 21, 21, 20, 5, 5, 1, 1, 13, 20, 20, 20, 20, 21, 25, 25, 25, 25, 20, 20] 25 rigid atoms, others: [2, 3, 4, 5, 6, 7, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113540 none O=C(CN1N=CC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 8, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 23, 25, 25, 25, 25, 6, 6, 6, 6, 6, 6, 5, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 23, 23, 25, 25, 12, 6, 6, 6, 6, 6, 5, 5, 2, 2, 6, 6] 25 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 91 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113540 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113540/1 /scratch/stefan/7770410/working/building/REAL300020113540 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 688) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/688 `/scratch/stefan/7770410/working/3D/688' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1N=CC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113540.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113540/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113540 none O=C(CN1N=CC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 8, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 18, 20, 20, 20, 20, 1, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 5, 5, 5, 4, 4, 1, 18, 18, 20, 20, 6, 1, 1, 1, 1, 4, 5, 5, 5, 5, 1, 1] 25 rigid atoms, others: [32, 33, 39, 8, 9, 10, 11, 12, 40, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38]) total number of confs: 75 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113540 none O=C(CN1N=CC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 8, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 19, 21, 21, 21, 21, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 4, 19, 19, 21, 21, 9, 4, 4, 4, 4, 1, 4, 4, 4, 4, 4, 4] 25 rigid atoms, others: [34, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 78 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113540 none O=C(CN1N=CC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 8, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 13, 13, 20, 20, 20, 21, 21, 21, 25, 25, 25, 25, 25, 25, 21, 21, 20, 5, 5, 1, 1, 13, 20, 20, 20, 20, 21, 25, 25, 25, 25, 20, 20] 25 rigid atoms, others: [2, 3, 4, 5, 6, 7, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113540 none O=C(CN1N=CC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 8, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 23, 25, 25, 25, 25, 6, 6, 6, 6, 6, 6, 5, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 23, 23, 25, 25, 12, 6, 6, 6, 6, 6, 5, 5, 2, 2, 6, 6] 25 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 91 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113540 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113540 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113540/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113540/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113540 Building REAL300020113541 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113541' /scratch/stefan/7770410/working/building/REAL300020113541 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113541 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113541/0 /scratch/stefan/7770410/working/building/REAL300020113541 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/689 `/scratch/stefan/7770410/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC(Cl)=N1) `REAL300020113541.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113541 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC(Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 16, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 19, 27, 28, 28, 28, 28, 6, 6, 1, 26, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 6, 19, 19, 27, 27, 1, 1] 77 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 39, 40, 21, 30, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38]) total number of confs: 145 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113541 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC(Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 16, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 8, 10, 11, 11, 11, 11, 1, 1, 6, 46, 46, 46, 46, 46, 46, 46, 19, 6, 6, 6, 6, 1, 8, 8, 10, 10, 6, 6] 77 rigid atoms, others: [34, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 124 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113541 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC(Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 16, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 26, 26, 26, 46, 46, 46, 69, 77, 77, 77, 77, 77, 46, 46, 26, 1, 1, 1, 1, 2, 2, 2, 9, 26, 26, 26, 26, 46, 69, 69, 77, 77, 26, 26] 77 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113541 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC(Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 16, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 47, 47, 47, 29, 29, 29, 13, 13, 13, 7, 3, 1, 1, 1, 1, 1, 1, 13, 13, 29, 77, 77, 77, 77, 77, 77, 77, 47, 29, 29, 29, 29, 13, 7, 7, 3, 3, 29, 29] 77 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 196 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113541 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113541/1 /scratch/stefan/7770410/working/building/REAL300020113541 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 690) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/690 `/scratch/stefan/7770410/working/3D/690' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC(Cl)=N1) `REAL300020113541.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113541 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC(Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 16, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 18, 26, 27, 27, 27, 27, 6, 6, 1, 26, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 6, 18, 18, 26, 26, 1, 1] 76 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 39, 40, 21, 30, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38]) total number of confs: 142 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113541 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC(Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 16, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 8, 10, 11, 11, 11, 11, 1, 1, 6, 46, 46, 46, 46, 46, 46, 46, 19, 6, 6, 6, 6, 1, 8, 8, 10, 10, 6, 6] 76 rigid atoms, others: [34, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 124 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113541 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC(Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 16, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 26, 26, 26, 46, 46, 46, 68, 76, 76, 76, 76, 76, 46, 46, 26, 1, 1, 1, 1, 2, 2, 2, 9, 26, 26, 26, 26, 46, 68, 68, 76, 76, 26, 26] 76 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 272 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113541 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC(Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 16, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 48, 48, 48, 30, 30, 30, 13, 13, 13, 7, 3, 1, 1, 1, 1, 1, 1, 13, 13, 30, 77, 77, 77, 77, 77, 77, 77, 48, 30, 30, 30, 30, 13, 7, 7, 3, 3, 30, 30] 77 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 198 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113541 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113541 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113541/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113541/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113541 Building REAL300020113542 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113542' /scratch/stefan/7770410/working/building/REAL300020113542 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113542 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113542/0 /scratch/stefan/7770410/working/building/REAL300020113542 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 691) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/691 `/scratch/stefan/7770410/working/3D/691' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1) `REAL300020113542.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113542 none CC1=CC(C)=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 32, 48, 55, 55, 55, 55, 11, 11, 1, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 11, 32, 32, 48, 48, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 239 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113542 none CC1=CC(C)=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 91, 91, 34, 34, 34, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 91, 91, 91, 91, 91, 91, 91, 91, 34, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 205 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113542 none CC1=CC(C)=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 20, 20, 20, 91, 91, 91, 145, 201, 201, 201, 201, 201, 91, 91, 20, 1, 2, 2, 2, 1, 2, 2, 2, 7, 20, 20, 20, 20, 91, 145, 145, 201, 201, 20, 20] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 769 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113542 none CC1=CC(C)=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 126, 126, 126, 56, 56, 56, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 56, 201, 201, 201, 201, 201, 201, 201, 201, 126, 56, 56, 56, 56, 11, 6, 6, 4, 4, 56, 56] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 487 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113542 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113542/1 /scratch/stefan/7770410/working/building/REAL300020113542 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 692) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/692 `/scratch/stefan/7770410/working/3D/692' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1) `REAL300020113542.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113542/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113542 none CC1=CC(C)=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 32, 48, 55, 55, 55, 55, 11, 11, 1, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 11, 32, 32, 48, 48, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 239 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113542 none CC1=CC(C)=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 91, 91, 34, 34, 34, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 91, 91, 91, 91, 91, 91, 91, 91, 34, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 205 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113542 none CC1=CC(C)=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 20, 20, 20, 91, 91, 91, 145, 201, 201, 201, 201, 201, 91, 91, 20, 1, 2, 2, 2, 1, 2, 2, 2, 7, 20, 20, 20, 20, 91, 145, 145, 201, 201, 20, 20] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 769 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113542 none CC1=CC(C)=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 126, 126, 126, 55, 55, 55, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 55, 201, 201, 201, 201, 201, 201, 201, 201, 126, 55, 55, 55, 55, 11, 6, 6, 4, 4, 55, 55] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 487 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113542 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113542 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113542/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113542/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113542 Building REAL300020113543 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113543' /scratch/stefan/7770410/working/building/REAL300020113543 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113543 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113543/0 /scratch/stefan/7770410/working/building/REAL300020113543 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 693) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/693 `/scratch/stefan/7770410/working/3D/693' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C2CCCCC2=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113543.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113543 none CN1N=C2CCCCC2=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 35, 53, 59, 59, 59, 59, 13, 13, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 1, 1, 1, 1, 13, 35, 35, 53, 53, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 275 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113543 none CN1N=C2CCCCC2=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 119, 119, 119, 119, 119, 119, 119, 59, 59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 119, 119, 119, 119, 119, 119, 119, 119, 119, 119, 119, 59, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 272 number of broken/clashed sets: 16 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113543 none CN1N=C2CCCCC2=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 28, 28, 28, 119, 119, 119, 170, 201, 201, 201, 201, 201, 119, 119, 28, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 9, 28, 28, 28, 28, 119, 170, 170, 201, 201, 28, 28] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 10, 7, 34, 35, 36, 33, 38, 39, 37] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 637 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113543 none CN1N=C2CCCCC2=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 158, 158, 158, 60, 60, 60, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 60, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 158, 60, 60, 60, 60, 11, 6, 6, 4, 4, 60, 60] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 507 number of broken/clashed sets: 16 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113543 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113543/1 /scratch/stefan/7770410/working/building/REAL300020113543 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 694) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/694 `/scratch/stefan/7770410/working/3D/694' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C2CCCCC2=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113543.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113543/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113543 none CN1N=C2CCCCC2=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 35, 53, 59, 59, 59, 59, 13, 13, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 1, 1, 1, 1, 13, 35, 35, 53, 53, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 275 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113543 none CN1N=C2CCCCC2=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 120, 120, 120, 120, 120, 120, 120, 59, 59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 120, 120, 120, 120, 120, 120, 120, 120, 120, 120, 120, 59, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 273 number of broken/clashed sets: 16 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113543 none CN1N=C2CCCCC2=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 28, 28, 28, 120, 120, 120, 170, 201, 201, 201, 201, 201, 120, 120, 28, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 9, 28, 28, 28, 28, 120, 170, 170, 201, 201, 28, 28] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 10, 7, 34, 35, 36, 33, 38, 39, 37] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 633 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113543 none CN1N=C2CCCCC2=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 157, 157, 157, 60, 60, 60, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 60, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 157, 60, 60, 60, 60, 11, 6, 6, 4, 4, 60, 60] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 506 number of broken/clashed sets: 15 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113543 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113543 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113543/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113543/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113543 Building REAL300020113544 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113544' /scratch/stefan/7770410/working/building/REAL300020113544 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113544 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113544/0 /scratch/stefan/7770410/working/building/REAL300020113544 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/695 `/scratch/stefan/7770410/working/3D/695' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113544.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113544 none CCCN1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 26, 11, 11, 11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 44, 49, 49, 49, 49, 11, 11, 1, 30, 30, 30, 30, 30, 26, 26, 11, 11, 6, 1, 1, 1, 1, 11, 31, 31, 44, 44, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 297 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113544 none CCCN1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 109, 58, 58, 58, 58, 58, 32, 32, 32, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 116, 116, 116, 116, 116, 109, 109, 58, 58, 32, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 484 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113544 none CCCN1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 58, 58, 58, 102, 125, 126, 126, 126, 126, 58, 58, 11, 8, 8, 8, 8, 8, 6, 6, 1, 1, 4, 11, 11, 11, 11, 58, 102, 102, 125, 125, 11, 11] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 34, 35] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 480 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113544 none CCCN1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 127, 127, 127, 127, 127, 107, 107, 107, 50, 50, 50, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 50, 201, 201, 201, 201, 201, 201, 201, 127, 127, 107, 50, 50, 50, 50, 11, 6, 6, 4, 4, 50, 50] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 785 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113544 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113544/1 /scratch/stefan/7770410/working/building/REAL300020113544 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 696) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/696 `/scratch/stefan/7770410/working/3D/696' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113544.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113544/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113544 none CCCN1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 26, 11, 11, 11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 44, 49, 49, 49, 49, 11, 11, 1, 30, 30, 30, 30, 30, 26, 26, 11, 11, 6, 1, 1, 1, 1, 11, 31, 31, 44, 44, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 297 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113544 none CCCN1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 108, 58, 58, 58, 58, 58, 32, 32, 32, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 114, 114, 114, 114, 114, 108, 108, 58, 58, 32, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 472 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113544 none CCCN1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 58, 58, 58, 101, 125, 126, 126, 126, 126, 58, 58, 11, 8, 8, 8, 8, 8, 6, 6, 1, 1, 4, 11, 11, 11, 11, 58, 101, 101, 125, 125, 11, 11] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 34, 35] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 480 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113544 none CCCN1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 128, 128, 128, 128, 128, 108, 108, 108, 51, 51, 51, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 51, 201, 201, 201, 201, 201, 201, 201, 128, 128, 108, 51, 51, 51, 51, 10, 6, 6, 4, 4, 51, 51] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 781 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113544 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113544 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113544/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113544/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113544 Building REAL300020113545 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113545' /scratch/stefan/7770410/working/building/REAL300020113545 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113545 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113545/0 /scratch/stefan/7770410/working/building/REAL300020113545 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/697 `/scratch/stefan/7770410/working/3D/697' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1) `REAL300020113545.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113545 none CCCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 10, 10, 10, 10, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 37, 52, 60, 60, 60, 60, 11, 11, 1, 10, 19, 19, 19, 19, 19, 19, 19, 10, 10, 6, 1, 1, 1, 1, 11, 37, 37, 52, 52, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 286 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113545 none CCCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 42, 42, 42, 42, 36, 36, 36, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 42, 82, 82, 82, 82, 82, 82, 82, 42, 42, 36, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 357 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113545 none CCCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 42, 42, 42, 86, 119, 122, 122, 122, 122, 42, 42, 10, 1, 5, 5, 5, 4, 4, 4, 4, 1, 1, 3, 10, 10, 10, 10, 42, 86, 86, 119, 119, 10, 10] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 2, 35, 26] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 501 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113545 none CCCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 122, 122, 122, 122, 121, 121, 121, 60, 60, 60, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 60, 122, 201, 201, 201, 201, 201, 201, 201, 122, 122, 121, 60, 60, 60, 60, 11, 6, 6, 4, 4, 60, 60] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 811 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113545 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113545/1 /scratch/stefan/7770410/working/building/REAL300020113545 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 698) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/698 `/scratch/stefan/7770410/working/3D/698' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1) `REAL300020113545.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113545/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113545 none CCCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 10, 10, 10, 10, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 37, 52, 60, 60, 60, 60, 11, 11, 1, 10, 19, 19, 19, 19, 19, 19, 19, 10, 10, 6, 1, 1, 1, 1, 11, 37, 37, 52, 52, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 286 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113545 none CCCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 42, 42, 42, 42, 36, 36, 36, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 42, 82, 82, 82, 82, 82, 82, 82, 42, 42, 36, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 357 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113545 none CCCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 42, 42, 42, 86, 119, 122, 122, 122, 122, 42, 42, 10, 1, 5, 5, 5, 4, 4, 4, 4, 1, 1, 3, 10, 10, 10, 10, 42, 86, 86, 119, 119, 10, 10] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 2, 35, 26] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 501 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113545 none CCCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 122, 122, 122, 122, 120, 120, 120, 59, 59, 59, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 59, 122, 201, 201, 201, 201, 201, 201, 201, 122, 122, 120, 59, 59, 59, 59, 12, 6, 6, 4, 4, 59, 59] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 810 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113545 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113545 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113545/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113545/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113545 Building REAL300020113546 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113546' /scratch/stefan/7770410/working/building/REAL300020113546 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113546 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113546/0 /scratch/stefan/7770410/working/building/REAL300020113546 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 699) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/699 `/scratch/stefan/7770410/working/3D/699' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C2CC2)=N1) `REAL300020113546.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113546 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 28, 42, 45, 45, 45, 45, 11, 11, 1, 19, 19, 38, 38, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 11, 28, 28, 42, 42, 1, 1, 38, 38, 38, 38, 38] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48]) total number of confs: 272 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113546 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 17, 17, 17, 38, 38, 38, 118, 118, 118, 166, 201, 201, 201, 201, 201, 118, 118, 38, 1, 1, 1, 1, 7, 7, 7, 7, 7, 17, 38, 38, 38, 38, 118, 166, 166, 201, 201, 38, 38, 1, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 48, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 671 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113546 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 31, 31, 31, 11, 11, 11, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 11, 88, 88, 118, 118, 88, 88, 88, 88, 88, 31, 11, 11, 11, 11, 1, 5, 5, 7, 7, 11, 11, 118, 118, 118, 118, 118] 201 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 300 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113546 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 88, 88, 88, 151, 192, 195, 195, 195, 195, 88, 88, 19, 1, 1, 7, 7, 1, 2, 2, 2, 1, 7, 19, 19, 19, 19, 88, 151, 151, 192, 192, 19, 19, 7, 7, 7, 7, 7] 201 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 27, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 714 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113546 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [195, 195, 195, 94, 94, 94, 45, 45, 45, 9, 9, 9, 6, 4, 1, 1, 1, 1, 1, 1, 9, 9, 45, 195, 195, 201, 201, 195, 195, 195, 195, 195, 94, 45, 45, 45, 45, 9, 6, 6, 4, 4, 45, 45, 201, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 451 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113546 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113546/1 /scratch/stefan/7770410/working/building/REAL300020113546 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 700) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/700 `/scratch/stefan/7770410/working/3D/700' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C2CC2)=N1) `REAL300020113546.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113546/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113546 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 28, 42, 45, 45, 45, 45, 11, 11, 1, 19, 19, 38, 38, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 11, 28, 28, 42, 42, 1, 1, 38, 38, 38, 38, 38] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48]) total number of confs: 272 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113546 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 17, 17, 17, 38, 38, 38, 117, 117, 117, 165, 201, 201, 201, 201, 201, 117, 117, 38, 1, 1, 1, 1, 7, 7, 7, 7, 7, 17, 38, 38, 38, 38, 117, 165, 165, 201, 201, 38, 38, 1, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 48, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 675 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113546 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 31, 31, 31, 11, 11, 11, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 11, 88, 88, 117, 117, 88, 88, 88, 88, 88, 31, 11, 11, 11, 11, 1, 5, 5, 7, 7, 11, 11, 117, 117, 117, 117, 117] 201 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 296 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113546 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 88, 88, 88, 150, 192, 195, 195, 195, 195, 88, 88, 19, 1, 1, 7, 7, 1, 2, 2, 2, 1, 7, 19, 19, 19, 19, 88, 150, 150, 192, 192, 19, 19, 7, 7, 7, 7, 7] 201 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 27, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 720 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113546 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [195, 195, 195, 93, 93, 93, 45, 45, 45, 9, 9, 9, 6, 4, 1, 1, 1, 1, 1, 1, 9, 9, 45, 195, 195, 201, 201, 195, 195, 195, 195, 195, 93, 45, 45, 45, 45, 9, 6, 6, 4, 4, 45, 45, 201, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 449 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113546 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113546 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113546/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113546/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113546 Building REAL300020113547 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113547' /scratch/stefan/7770410/working/building/REAL300020113547 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113547 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113547/0 /scratch/stefan/7770410/working/building/REAL300020113547 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/701 `/scratch/stefan/7770410/working/3D/701' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C2CC2)=N1) `REAL300020113547.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113547 none CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 13, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 25, 37, 37, 37, 37, 37, 8, 8, 1, 13, 13, 21, 21, 13, 24, 24, 24, 24, 24, 13, 5, 1, 1, 1, 1, 8, 25, 25, 37, 37, 1, 1, 21, 21, 21, 21, 21] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 45, 46, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51]) total number of confs: 264 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113547 none CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 5, 5, 5, 5, 8, 8, 8, 21, 21, 21, 84, 84, 84, 149, 201, 201, 201, 201, 201, 84, 84, 21, 1, 1, 1, 1, 5, 10, 10, 10, 10, 10, 5, 8, 21, 21, 21, 21, 84, 149, 149, 201, 201, 21, 21, 1, 1, 1, 1, 1] 201 rigid atoms, others: [47, 48, 49, 50, 51, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 788 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113547 none CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 56, 56, 56, 22, 22, 22, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 56, 56, 84, 84, 56, 93, 93, 93, 93, 93, 56, 22, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 84, 84, 84, 84, 84] 201 rigid atoms, others: [40, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 467 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113547 none CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 56, 56, 56, 105, 142, 142, 142, 142, 142, 56, 56, 13, 1, 1, 5, 5, 1, 5, 5, 5, 5, 5, 1, 4, 13, 13, 13, 13, 56, 105, 105, 142, 142, 13, 13, 5, 5, 5, 5, 5] 201 rigid atoms, others: [1, 2, 3, 4, 5, 34, 24, 25, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 568 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113547 none CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 146, 146, 146, 69, 69, 69, 40, 40, 40, 11, 11, 11, 4, 2, 1, 1, 1, 1, 1, 1, 11, 11, 40, 146, 146, 201, 201, 146, 201, 201, 201, 201, 201, 146, 69, 40, 40, 40, 40, 11, 4, 4, 2, 2, 40, 40, 201, 201, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 860 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113547 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113547/1 /scratch/stefan/7770410/working/building/REAL300020113547 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 702) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/702 `/scratch/stefan/7770410/working/3D/702' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C2CC2)=N1) `REAL300020113547.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113547 none CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 14, 13, 14, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 25, 37, 37, 37, 37, 37, 8, 8, 1, 14, 14, 22, 22, 14, 25, 25, 25, 25, 25, 14, 5, 1, 1, 1, 1, 8, 25, 25, 37, 37, 1, 1, 22, 22, 22, 22, 22] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 45, 46, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51]) total number of confs: 270 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113547 none CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 5, 5, 5, 5, 8, 8, 8, 22, 22, 22, 85, 85, 85, 150, 201, 201, 201, 201, 201, 85, 85, 22, 1, 1, 1, 1, 5, 10, 10, 10, 10, 10, 5, 8, 22, 22, 22, 22, 85, 150, 150, 201, 201, 22, 22, 1, 1, 1, 1, 1] 201 rigid atoms, others: [47, 48, 49, 50, 51, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 784 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113547 none CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 57, 57, 57, 22, 22, 22, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 57, 57, 85, 85, 57, 94, 94, 94, 94, 94, 57, 22, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 85, 85, 85, 85, 85] 201 rigid atoms, others: [40, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 468 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113547 none CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 57, 57, 57, 106, 142, 142, 142, 142, 142, 57, 57, 14, 1, 1, 5, 5, 1, 5, 5, 5, 5, 5, 1, 4, 14, 14, 14, 14, 57, 106, 106, 142, 142, 14, 14, 5, 5, 5, 5, 5] 201 rigid atoms, others: [1, 2, 3, 4, 5, 34, 24, 25, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 564 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113547 none CCN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 146, 146, 146, 68, 68, 68, 39, 39, 39, 11, 11, 11, 5, 3, 1, 1, 1, 1, 1, 1, 11, 11, 39, 146, 146, 201, 201, 146, 201, 201, 201, 201, 201, 146, 68, 39, 39, 39, 39, 11, 5, 5, 3, 3, 39, 39, 201, 201, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 861 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113547 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113547 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113547/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113547/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113547 Building REAL300020113548 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113548' /scratch/stefan/7770410/working/building/REAL300020113548 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113548 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113548/0 /scratch/stefan/7770410/working/building/REAL300020113548 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/703 `/scratch/stefan/7770410/working/3D/703' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=NN1C) `REAL300020113548.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113548 none CC1=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 24, 23, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 20, 32, 32, 32, 32, 32, 8, 8, 1, 38, 38, 38, 38, 38, 38, 38, 24, 24, 23, 23, 5, 1, 1, 1, 1, 8, 20, 20, 32, 32, 1, 1, 38, 38, 38, 38] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 45, 46, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50]) total number of confs: 245 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113548 none CC1=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 77, 77, 19, 19, 19, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 114, 114, 114, 114, 114, 114, 114, 77, 77, 77, 77, 19, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8, 114, 114, 114, 114] 201 rigid atoms, others: [40, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 368 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113548 none CC1=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 21, 21, 21, 38, 38, 38, 114, 114, 114, 157, 201, 201, 201, 201, 201, 114, 114, 38, 1, 1, 1, 1, 2, 2, 2, 3, 3, 5, 5, 21, 38, 38, 38, 38, 114, 157, 157, 201, 201, 38, 38, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 47, 24, 25, 26, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50]) total number of confs: 732 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113548 none CC1=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 137, 137, 48, 48, 48, 32, 32, 32, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 32, 201, 201, 201, 201, 201, 201, 201, 137, 137, 137, 137, 48, 32, 32, 32, 32, 7, 4, 4, 2, 2, 32, 32, 201, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 640 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113548 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113548/1 /scratch/stefan/7770410/working/building/REAL300020113548 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 704) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/704 `/scratch/stefan/7770410/working/3D/704' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=NN1C) `REAL300020113548.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113548 none CC1=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 24, 23, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 20, 32, 32, 32, 32, 32, 8, 8, 1, 38, 38, 38, 38, 38, 38, 38, 24, 24, 23, 23, 5, 1, 1, 1, 1, 8, 20, 20, 32, 32, 1, 1, 38, 38, 38, 38] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 45, 46, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50]) total number of confs: 245 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113548 none CC1=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 77, 77, 19, 19, 19, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 114, 114, 114, 114, 114, 114, 114, 77, 77, 77, 77, 19, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8, 114, 114, 114, 114] 201 rigid atoms, others: [40, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 368 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113548 none CC1=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 21, 21, 21, 38, 38, 38, 114, 114, 114, 156, 201, 201, 201, 201, 201, 114, 114, 38, 1, 1, 1, 1, 2, 2, 2, 3, 3, 5, 5, 21, 38, 38, 38, 38, 114, 156, 156, 201, 201, 38, 38, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 47, 24, 25, 26, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50]) total number of confs: 732 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113548 none CC1=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 138, 138, 48, 48, 48, 32, 32, 32, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 32, 201, 201, 201, 201, 201, 201, 201, 138, 138, 138, 138, 48, 32, 32, 32, 32, 7, 4, 4, 2, 2, 32, 32, 201, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 644 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113548 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113548 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113548/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113548/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113548 Building REAL300020113549 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113549' /scratch/stefan/7770410/working/building/REAL300020113549 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113549 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113549/0 /scratch/stefan/7770410/working/building/REAL300020113549 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/705 `/scratch/stefan/7770410/working/3D/705' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020113549.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113549 none COC1=NOC(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [97, 94, 94, 94, 94, 53, 39, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 18, 26, 28, 28, 28, 28, 5, 5, 1, 94, 97, 97, 97, 53, 53, 39, 39, 6, 1, 1, 1, 1, 5, 18, 18, 26, 26, 1, 1, 94] 158 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47]) total number of confs: 396 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113549 none COC1=NOC(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [121, 118, 118, 118, 118, 88, 75, 16, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 5, 118, 121, 121, 121, 88, 88, 75, 75, 16, 5, 5, 5, 5, 1, 7, 7, 9, 9, 5, 5, 118] 158 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 433 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113549 none COC1=NOC(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 7, 13, 48, 49, 49, 94, 94, 94, 118, 118, 118, 143, 157, 158, 158, 158, 158, 118, 118, 94, 1, 3, 3, 3, 7, 7, 13, 13, 49, 94, 94, 94, 94, 118, 143, 143, 157, 157, 94, 94, 1] 158 rigid atoms, others: [1, 2, 3, 4, 5, 6, 47, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 549 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113549 none COC1=NOC(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 166, 155, 53, 53, 53, 36, 36, 36, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 36, 201, 201, 201, 201, 166, 166, 155, 155, 53, 36, 36, 36, 36, 15, 6, 6, 4, 4, 36, 36, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 696 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113549 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113549/1 /scratch/stefan/7770410/working/building/REAL300020113549 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 706) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/706 `/scratch/stefan/7770410/working/3D/706' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020113549.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113549 none COC1=NOC(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [96, 93, 93, 93, 93, 53, 39, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 18, 26, 28, 28, 28, 28, 5, 5, 1, 93, 96, 96, 96, 53, 53, 39, 39, 6, 1, 1, 1, 1, 5, 18, 18, 26, 26, 1, 1, 93] 155 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47]) total number of confs: 395 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113549 none COC1=NOC(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [120, 117, 117, 117, 117, 88, 75, 16, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 5, 117, 120, 120, 120, 88, 88, 75, 75, 16, 5, 5, 5, 5, 1, 7, 7, 9, 9, 5, 5, 117] 155 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 431 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113549 none COC1=NOC(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 7, 13, 48, 49, 49, 93, 93, 93, 117, 117, 117, 141, 154, 155, 155, 155, 155, 117, 117, 93, 1, 3, 3, 3, 7, 7, 13, 13, 49, 93, 93, 93, 93, 117, 141, 141, 154, 154, 93, 93, 1] 155 rigid atoms, others: [1, 2, 3, 4, 5, 6, 47, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 533 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113549 none COC1=NOC(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 164, 153, 52, 52, 52, 34, 34, 34, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 34, 201, 201, 201, 201, 164, 164, 153, 153, 52, 34, 34, 34, 34, 13, 6, 6, 4, 4, 34, 34, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 696 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113549 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113549 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113549/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113549/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113549 Building REAL300020113550 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113550' /scratch/stefan/7770410/working/building/REAL300020113550 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113550 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113550/0 /scratch/stefan/7770410/working/building/REAL300020113550 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/707 `/scratch/stefan/7770410/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2N=CN=C2NC=C1) `REAL300020113550.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113550 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2N=CN=C2NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 12, 52, 98, 98, 98, 98, 98, 98, 98, 98, 52, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 98, 98, 98, 98] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 250 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113550 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2N=CN=C2NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 103, 103, 103, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 103, 189, 201, 201, 201, 201, 201, 201, 201, 201, 189, 103, 103, 103, 103, 18, 6, 6, 4, 4, 103, 103, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 544 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113550 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2N=CN=C2NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 65, 83, 102, 102, 102, 102, 12, 12, 1, 6, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 12, 65, 65, 83, 83, 1, 1, 20, 20, 20, 20] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 379 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113550 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2N=CN=C2NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 20, 20, 20, 98, 98, 98, 180, 201, 201, 201, 201, 201, 98, 98, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 20, 20, 20, 20, 98, 180, 180, 201, 201, 20, 20, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 682 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113550 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113550/1 /scratch/stefan/7770410/working/building/REAL300020113550 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 708) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/708 `/scratch/stefan/7770410/working/3D/708' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2N=CN=C2NC=C1) `REAL300020113550.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113550 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2N=CN=C2NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 12, 52, 98, 98, 98, 98, 98, 98, 98, 98, 52, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 98, 98, 98, 98] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 248 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113550 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2N=CN=C2NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 103, 103, 103, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 103, 189, 201, 201, 201, 201, 201, 201, 201, 201, 189, 103, 103, 103, 103, 18, 6, 6, 4, 4, 103, 103, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 544 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113550 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2N=CN=C2NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 66, 84, 103, 103, 103, 103, 12, 12, 1, 6, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 12, 66, 66, 84, 84, 1, 1, 20, 20, 20, 20] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 382 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113550 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2N=CN=C2NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 20, 20, 20, 98, 98, 98, 180, 201, 201, 201, 201, 201, 98, 98, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 20, 20, 20, 20, 98, 180, 180, 201, 201, 20, 20, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 682 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113550 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113550 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113550/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113550/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113550 Building REAL300020113551 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113551' /scratch/stefan/7770410/working/building/REAL300020113551 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113551 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113551/0 /scratch/stefan/7770410/working/building/REAL300020113551 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/709 `/scratch/stefan/7770410/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C)=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113551.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113551 none CC1=CC=CC(C)=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 37, 52, 57, 57, 57, 57, 11, 11, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 1, 1, 1, 1, 11, 37, 37, 52, 52, 1, 1] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 298 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113551 none CC1=CC=CC(C)=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 106, 106, 106, 106, 106, 38, 38, 38, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 38, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 403 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113551 none CC1=CC=CC(C)=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 12, 12, 12, 27, 27, 27, 105, 105, 105, 172, 201, 201, 201, 201, 201, 105, 105, 27, 2, 2, 2, 1, 1, 1, 2, 2, 2, 3, 3, 12, 27, 27, 27, 27, 105, 172, 172, 201, 201, 27, 27] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 33, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 708 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113551 none CC1=CC=CC(C)=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 113, 113, 113, 55, 55, 55, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 55, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 113, 55, 55, 55, 55, 12, 6, 6, 4, 4, 55, 55] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 709 number of broken/clashed sets: 201 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113551 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113551/1 /scratch/stefan/7770410/working/building/REAL300020113551 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 710) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/710 `/scratch/stefan/7770410/working/3D/710' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C)=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113551.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113551 none CC1=CC=CC(C)=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 37, 52, 57, 57, 57, 57, 11, 11, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 1, 1, 1, 1, 11, 37, 37, 52, 52, 1, 1] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 298 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113551 none CC1=CC=CC(C)=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 107, 107, 107, 107, 38, 38, 38, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 38, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 406 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113551 none CC1=CC=CC(C)=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 12, 12, 12, 27, 27, 27, 105, 105, 105, 172, 201, 201, 201, 201, 201, 105, 105, 27, 2, 2, 2, 1, 1, 1, 2, 2, 2, 3, 3, 12, 27, 27, 27, 27, 105, 172, 172, 201, 201, 27, 27] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 33, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 708 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113551 none CC1=CC=CC(C)=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 113, 113, 113, 57, 57, 57, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 57, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 113, 57, 57, 57, 57, 12, 6, 6, 4, 4, 57, 57] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 712 number of broken/clashed sets: 201 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113551 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113551 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113551/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113551/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113551 Building REAL300020113552 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113552' /scratch/stefan/7770410/working/building/REAL300020113552 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113552 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113552/0 /scratch/stefan/7770410/working/building/REAL300020113552 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 711) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/711 `/scratch/stefan/7770410/working/3D/711' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1C=CC=CC=C1) `REAL300020113552.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113552 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1C=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 13, 57, 97, 97, 97, 97, 97, 97, 57, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 97, 97, 97, 97, 97, 97, 97] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 331 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113552 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1C=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [153, 153, 56, 56, 56, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 56, 153, 201, 201, 201, 201, 201, 201, 153, 56, 56, 56, 56, 9, 5, 5, 3, 3, 56, 56, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 610 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113552 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1C=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 38, 55, 56, 56, 56, 56, 13, 13, 1, 6, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 13, 38, 38, 55, 55, 1, 1, 11, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113552 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1C=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 11, 11, 11, 97, 97, 97, 169, 201, 201, 201, 201, 201, 97, 97, 11, 1, 1, 1, 1, 1, 1, 1, 3, 11, 11, 11, 11, 97, 169, 169, 201, 201, 11, 11, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 38, 39, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 681 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113552 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113552/1 /scratch/stefan/7770410/working/building/REAL300020113552 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 712) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/712 `/scratch/stefan/7770410/working/3D/712' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1C=CC=CC=C1) `REAL300020113552.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113552 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1C=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 13, 57, 97, 97, 97, 97, 97, 97, 57, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 97, 97, 97, 97, 97, 97, 97] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 331 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113552 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1C=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [153, 153, 56, 56, 56, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 56, 153, 201, 201, 201, 201, 201, 201, 153, 56, 56, 56, 56, 9, 5, 5, 3, 3, 56, 56, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 610 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113552 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1C=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 38, 55, 56, 56, 56, 56, 13, 13, 1, 6, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 13, 38, 38, 55, 55, 1, 1, 11, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113552 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1C=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 11, 11, 11, 97, 97, 97, 169, 201, 201, 201, 201, 201, 97, 97, 11, 1, 1, 1, 1, 1, 1, 1, 3, 11, 11, 11, 11, 97, 169, 169, 201, 201, 11, 11, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 38, 39, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 681 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113552 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113552 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113552/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113552/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113552 Building REAL300020113553 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113553' /scratch/stefan/7770410/working/building/REAL300020113553 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113553 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113553/0 /scratch/stefan/7770410/working/building/REAL300020113553 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 713) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/713 `/scratch/stefan/7770410/working/3D/713' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113553.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113553 none C=C(C)CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [131, 101, 131, 87, 20, 20, 20, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 11, 11, 11, 11, 1, 1, 9, 131, 131, 131, 131, 131, 101, 101, 87, 87, 20, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 533 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113553 none C=C(C)CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 40, 21, 21, 21, 21, 21, 21, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 9, 9, 21, 56, 56, 56, 56, 56, 56, 56, 40, 40, 21, 21, 21, 21, 21, 9, 4, 4, 4, 4, 21, 21] 56 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 230 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113553 none C=C(C)CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 35, 65, 25, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 30, 36, 48, 48, 48, 48, 9, 9, 1, 65, 65, 65, 65, 65, 35, 35, 25, 25, 5, 1, 1, 1, 1, 9, 30, 30, 36, 36, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 398 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113553 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113553/1 /scratch/stefan/7770410/working/building/REAL300020113553 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 714) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/714 `/scratch/stefan/7770410/working/3D/714' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113553.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113553 none C=C(C)CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [131, 101, 131, 87, 20, 20, 20, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 11, 11, 11, 11, 1, 1, 9, 131, 131, 131, 131, 131, 101, 101, 87, 87, 20, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 533 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113553 none C=C(C)CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 40, 21, 21, 21, 21, 21, 21, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 9, 9, 21, 56, 56, 56, 56, 56, 56, 56, 40, 40, 21, 21, 21, 21, 21, 9, 4, 4, 4, 4, 21, 21] 56 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 230 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113553 none C=C(C)CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 35, 65, 25, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 30, 36, 48, 48, 48, 48, 9, 9, 1, 65, 65, 65, 65, 65, 35, 35, 25, 25, 5, 1, 1, 1, 1, 9, 30, 30, 36, 36, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 398 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113553 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113553 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113553/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113553/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113553 Building REAL300020113554 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113554' /scratch/stefan/7770410/working/building/REAL300020113554 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for REAL300020113554 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113554/0 /scratch/stefan/7770410/working/building/REAL300020113554 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 715) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/715 `/scratch/stefan/7770410/working/3D/715' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CNC2=NC=NC2=C1) `REAL300020113554.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113554 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CNC2=NC=NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 37, 88, 88, 88, 88, 88, 88, 88, 88, 37, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 88, 88, 88, 88] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 206 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113554 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CNC2=NC=NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 61, 61, 61, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 61, 113, 201, 201, 201, 201, 201, 201, 201, 201, 113, 61, 61, 61, 61, 13, 6, 6, 4, 4, 61, 61, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 473 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113554 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CNC2=NC=NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 35, 51, 59, 59, 59, 59, 11, 11, 1, 6, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 11, 35, 35, 51, 51, 1, 1, 19, 19, 19, 19] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113554 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CNC2=NC=NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 19, 19, 19, 88, 88, 88, 161, 201, 201, 201, 201, 201, 88, 88, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 19, 19, 19, 19, 88, 161, 161, 201, 201, 19, 19, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 752 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113554 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113554/1 /scratch/stefan/7770410/working/building/REAL300020113554 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 716) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/716 `/scratch/stefan/7770410/working/3D/716' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CNC2=NC=NC2=C1) `REAL300020113554.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113554 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CNC2=NC=NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 36, 87, 87, 87, 87, 87, 87, 87, 87, 36, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 87, 87, 87, 87] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 204 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113554 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CNC2=NC=NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 63, 63, 63, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 63, 113, 201, 201, 201, 201, 201, 201, 201, 201, 113, 63, 63, 63, 63, 14, 6, 6, 4, 4, 63, 63, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 469 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113554 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CNC2=NC=NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 35, 51, 59, 59, 59, 59, 11, 11, 1, 6, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 11, 35, 35, 51, 51, 1, 1, 19, 19, 19, 19] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113554 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CNC2=NC=NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 19, 19, 19, 87, 87, 87, 159, 201, 201, 201, 201, 201, 87, 87, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 19, 19, 19, 19, 87, 159, 159, 201, 201, 19, 19, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 760 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113554 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `2' /scratch/stefan/7770410/working/building/REAL300020113554/2 /scratch/stefan/7770410/working/building/REAL300020113554 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 2 (index: 717) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/717 `/scratch/stefan/7770410/working/3D/717' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2NC=NC2=C1) `REAL300020113554.mol2' -> `2.mol2' `temp.mol2' -> `REAL300020113554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113554/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113554 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2NC=NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 11, 43, 97, 97, 97, 97, 97, 97, 97, 97, 43, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 97, 97, 97, 97] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 238 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113554 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2NC=NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 70, 70, 70, 15, 15, 15, 7, 4, 1, 1, 1, 1, 1, 1, 15, 15, 70, 120, 201, 201, 201, 201, 201, 201, 201, 201, 120, 70, 70, 70, 70, 15, 7, 7, 4, 4, 70, 70, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 480 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113554 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2NC=NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 40, 57, 68, 68, 68, 68, 11, 11, 1, 6, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 11, 40, 40, 57, 57, 1, 1, 18, 18, 18, 18] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113554 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2NC=NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 18, 18, 18, 97, 97, 97, 168, 201, 201, 201, 201, 201, 97, 97, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 18, 18, 18, 18, 97, 168, 168, 201, 201, 18, 18, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 696 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113554 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `3' /scratch/stefan/7770410/working/building/REAL300020113554/3 /scratch/stefan/7770410/working/building/REAL300020113554 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 3 (index: 718) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/718 `/scratch/stefan/7770410/working/3D/718' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2NC=NC2=C1) `REAL300020113554.mol2' -> `3.mol2' `temp.mol2' -> `REAL300020113554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113554/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113554 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2NC=NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 11, 43, 97, 97, 97, 97, 97, 97, 97, 97, 43, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 97, 97, 97, 97] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 239 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113554 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2NC=NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 68, 68, 68, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 68, 119, 201, 201, 201, 201, 201, 201, 201, 201, 119, 68, 68, 68, 68, 14, 6, 6, 4, 4, 68, 68, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 478 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113554 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2NC=NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 40, 57, 68, 68, 68, 68, 11, 11, 1, 6, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 11, 40, 40, 57, 57, 1, 1, 18, 18, 18, 18] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113554 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2NC=NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 18, 18, 18, 97, 97, 97, 169, 201, 201, 201, 201, 201, 97, 97, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 18, 18, 18, 18, 97, 169, 169, 201, 201, 18, 18, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 693 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113554 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113554 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 2: /scratch/stefan/7770410/working/building/REAL300020113554/2.* 1: /scratch/stefan/7770410/working/building/REAL300020113554/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113554/0.* 3: /scratch/stefan/7770410/working/building/REAL300020113554/3.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113554 Building REAL300020113555 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113555' /scratch/stefan/7770410/working/building/REAL300020113555 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113555 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113555/0 /scratch/stefan/7770410/working/building/REAL300020113555 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 719) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/719 `/scratch/stefan/7770410/working/3D/719' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CC=NC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113555.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113555 none O=C(CCC1=CC=NC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 8, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 22, 27, 46, 46, 46, 46, 46, 1, 1, 1, 1, 1, 10, 10, 10, 27, 41, 42, 42, 42, 42, 10, 10, 1, 22, 22, 27, 27, 46, 46, 46, 6, 1, 1, 1, 1, 10, 27, 27, 41, 41, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 44, 10, 11, 12, 13, 14, 45, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 306 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113555 none O=C(CCC1=CC=NC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 8, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 86, 98, 119, 119, 119, 119, 119, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 10, 86, 86, 98, 98, 119, 119, 119, 34, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10] 201 rigid atoms, others: [39, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 445 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113555 none O=C(CCC1=CC=NC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 8, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 10, 6, 1, 1, 1, 1, 1, 1, 1, 25, 25, 46, 46, 46, 119, 119, 119, 173, 201, 201, 201, 201, 201, 119, 119, 46, 10, 10, 6, 6, 1, 1, 1, 25, 46, 46, 46, 46, 119, 173, 173, 201, 201, 46, 46] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 708 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113555 none O=C(CCC1=CC=NC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 8, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 185, 200, 201, 201, 201, 201, 201, 40, 40, 40, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 40, 185, 185, 200, 200, 201, 201, 201, 101, 40, 40, 40, 40, 9, 4, 4, 2, 2, 40, 40] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 735 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113555 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113555/1 /scratch/stefan/7770410/working/building/REAL300020113555 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 720) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/720 `/scratch/stefan/7770410/working/3D/720' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CC=NC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113555.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113555 none O=C(CCC1=CC=NC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 8, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 22, 27, 46, 46, 46, 46, 46, 1, 1, 1, 1, 1, 10, 10, 10, 27, 41, 42, 42, 42, 42, 10, 10, 1, 22, 22, 27, 27, 46, 46, 46, 6, 1, 1, 1, 1, 10, 27, 27, 41, 41, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 44, 10, 11, 12, 13, 14, 45, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 306 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113555 none O=C(CCC1=CC=NC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 8, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 86, 99, 120, 120, 120, 120, 120, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 10, 86, 86, 99, 99, 120, 120, 120, 34, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10] 201 rigid atoms, others: [39, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 451 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113555 none O=C(CCC1=CC=NC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 8, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 10, 6, 1, 1, 1, 1, 1, 1, 1, 25, 25, 46, 46, 46, 120, 120, 120, 173, 201, 201, 201, 201, 201, 120, 120, 46, 10, 10, 6, 6, 1, 1, 1, 25, 46, 46, 46, 46, 120, 173, 173, 201, 201, 46, 46] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 706 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113555 none O=C(CCC1=CC=NC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 8, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 185, 200, 201, 201, 201, 201, 201, 39, 39, 39, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 39, 185, 185, 200, 200, 201, 201, 201, 100, 39, 39, 39, 39, 8, 4, 4, 2, 2, 39, 39] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 739 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113555 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113555 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113555/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113555/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113555 Building REAL300020113556 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113556' /scratch/stefan/7770410/working/building/REAL300020113556 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113556 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113556/0 /scratch/stefan/7770410/working/building/REAL300020113556 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/721 `/scratch/stefan/7770410/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1) `REAL300020113556.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113556 none CC(C)CN1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 7, 7, 7, 7, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 36, 54, 58, 58, 58, 58, 11, 11, 1, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 7, 6, 1, 1, 1, 1, 11, 36, 36, 54, 54, 1, 1] 201 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 49, 50, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 304 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113556 none CC(C)CN1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 47, 47, 47, 47, 46, 46, 46, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 47, 106, 106, 106, 106, 106, 106, 106, 106, 106, 47, 47, 46, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [44, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 446 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113556 none CC(C)CN1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 47, 47, 47, 104, 125, 129, 129, 129, 129, 47, 47, 7, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 3, 7, 7, 7, 7, 47, 104, 104, 125, 125, 7, 7] 201 rigid atoms, others: [3, 4, 5, 6, 7, 38, 8, 27, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 490 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113556 none CC(C)CN1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 129, 129, 129, 129, 128, 128, 128, 58, 58, 58, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 58, 129, 201, 201, 201, 201, 201, 201, 201, 201, 201, 129, 129, 128, 58, 58, 58, 58, 10, 6, 6, 4, 4, 58, 58] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 793 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113556 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113556/1 /scratch/stefan/7770410/working/building/REAL300020113556 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 722) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/722 `/scratch/stefan/7770410/working/3D/722' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1) `REAL300020113556.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113556 none CC(C)CN1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 7, 7, 7, 7, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 36, 54, 58, 58, 58, 58, 11, 11, 1, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 7, 6, 1, 1, 1, 1, 11, 36, 36, 54, 54, 1, 1] 201 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 49, 50, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 304 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113556 none CC(C)CN1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 47, 47, 47, 47, 46, 46, 46, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 47, 107, 107, 107, 107, 107, 107, 107, 107, 107, 47, 47, 46, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [44, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 449 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113556 none CC(C)CN1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 47, 47, 47, 103, 124, 128, 128, 128, 128, 47, 47, 7, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 3, 7, 7, 7, 7, 47, 103, 103, 124, 124, 7, 7] 201 rigid atoms, others: [3, 4, 5, 6, 7, 38, 8, 27, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 487 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113556 none CC(C)CN1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 128, 128, 128, 128, 127, 127, 127, 58, 58, 58, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 58, 128, 201, 201, 201, 201, 201, 201, 201, 201, 201, 128, 128, 127, 58, 58, 58, 58, 10, 6, 6, 4, 4, 58, 58] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 795 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113556 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113556 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113556/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113556/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113556 Building REAL300020113557 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113557' /scratch/stefan/7770410/working/building/REAL300020113557 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113557 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113557/0 /scratch/stefan/7770410/working/building/REAL300020113557 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 723) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/723 `/scratch/stefan/7770410/working/3D/723' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN(C2CCCC2)C=C1) `REAL300020113557.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113557 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN(C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 13, 51, 56, 56, 56, 92, 92, 92, 92, 56, 56, 51, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13, 92, 92, 92, 92, 92, 92, 92, 92, 92, 56, 56] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 301 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113557 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN(C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 6, 8, 8, 22, 22, 22, 92, 92, 92, 169, 201, 201, 201, 201, 201, 92, 92, 22, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 8, 22, 22, 22, 22, 92, 169, 169, 201, 201, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 201 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 714 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113557 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN(C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [186, 186, 77, 77, 77, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 77, 186, 192, 192, 192, 201, 201, 201, 201, 192, 192, 186, 77, 77, 77, 77, 14, 6, 6, 4, 4, 77, 77, 201, 201, 201, 201, 201, 201, 201, 201, 201, 192, 192] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 547 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113557 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN(C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 46, 64, 76, 76, 76, 76, 13, 13, 1, 6, 8, 8, 8, 22, 22, 22, 22, 8, 8, 6, 1, 1, 1, 1, 13, 46, 46, 64, 64, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 329 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113557 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN(C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 56, 56, 56, 136, 182, 191, 191, 191, 191, 56, 56, 8, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 3, 8, 8, 8, 8, 56, 136, 136, 182, 182, 8, 8, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1] 201 rigid atoms, others: [1, 51, 50, 19, 20, 21, 22, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 755 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113557 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113557/1 /scratch/stefan/7770410/working/building/REAL300020113557 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 724) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/724 `/scratch/stefan/7770410/working/3D/724' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN(C2CCCC2)C=C1) `REAL300020113557.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113557 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN(C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 13, 52, 57, 57, 57, 92, 92, 92, 92, 57, 57, 52, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13, 92, 92, 92, 92, 92, 92, 92, 92, 92, 57, 57] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 303 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113557 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN(C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 6, 8, 8, 21, 21, 21, 92, 92, 92, 169, 201, 201, 201, 201, 201, 92, 92, 21, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 8, 21, 21, 21, 21, 92, 169, 169, 201, 201, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 201 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 713 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113557 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN(C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [186, 186, 77, 77, 77, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 77, 186, 193, 193, 193, 201, 201, 201, 201, 193, 193, 186, 77, 77, 77, 77, 14, 6, 6, 4, 4, 77, 77, 201, 201, 201, 201, 201, 201, 201, 201, 201, 193, 193] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 545 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113557 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN(C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 46, 64, 76, 76, 76, 76, 13, 13, 1, 6, 8, 8, 8, 21, 21, 21, 21, 8, 8, 6, 1, 1, 1, 1, 13, 46, 46, 64, 64, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113557 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN(C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 57, 57, 57, 137, 183, 192, 192, 192, 192, 57, 57, 8, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 3, 8, 8, 8, 8, 57, 137, 137, 183, 183, 8, 8, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1] 201 rigid atoms, others: [1, 51, 50, 19, 20, 21, 22, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 756 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113557 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113557 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113557/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113557/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113557 Building REAL300020113558 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113558' /scratch/stefan/7770410/working/building/REAL300020113558 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113558 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113558/0 /scratch/stefan/7770410/working/building/REAL300020113558 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 725) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/725 `/scratch/stefan/7770410/working/3D/725' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)N1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113558.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113558 none CCC(C)N1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [40, 38, 22, 38, 22, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 16, 24, 24, 24, 24, 24, 5, 5, 1, 40, 40, 40, 40, 40, 38, 38, 38, 38, 22, 22, 6, 1, 1, 1, 1, 5, 16, 16, 24, 24, 1, 1] 94 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 231 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113558 none CCC(C)N1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 46, 59, 46, 46, 46, 46, 18, 18, 18, 5, 5, 5, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 5, 59, 59, 59, 59, 59, 59, 59, 59, 59, 46, 46, 18, 5, 5, 5, 5, 1, 6, 6, 8, 8, 5, 5] 94 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 194 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113558 none CCC(C)N1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 22, 22, 22, 46, 46, 46, 70, 85, 85, 85, 85, 85, 46, 46, 22, 7, 7, 7, 7, 7, 4, 4, 4, 4, 1, 1, 7, 22, 22, 22, 22, 46, 70, 70, 85, 85, 22, 22] 94 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 326 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113558 none CCC(C)N1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 83, 93, 83, 83, 83, 83, 45, 45, 45, 25, 25, 25, 9, 9, 9, 5, 2, 1, 1, 1, 1, 1, 1, 9, 9, 25, 93, 93, 93, 93, 93, 93, 93, 93, 93, 83, 83, 45, 25, 25, 25, 25, 9, 5, 5, 2, 2, 25, 25] 93 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 263 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113558 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113558/1 /scratch/stefan/7770410/working/building/REAL300020113558 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 726) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/726 `/scratch/stefan/7770410/working/3D/726' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)N1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113558.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113558 none CCC(C)N1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [41, 39, 22, 39, 22, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 16, 24, 24, 24, 24, 24, 5, 5, 1, 41, 41, 41, 41, 41, 39, 39, 39, 39, 22, 22, 6, 1, 1, 1, 1, 5, 16, 16, 24, 24, 1, 1] 97 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 234 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113558 none CCC(C)N1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 47, 61, 47, 47, 47, 47, 19, 19, 19, 5, 5, 5, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 5, 61, 61, 61, 61, 61, 61, 61, 61, 61, 47, 47, 19, 5, 5, 5, 5, 1, 6, 6, 8, 8, 5, 5] 97 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 202 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113558 none CCC(C)N1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 22, 22, 22, 47, 47, 47, 71, 87, 87, 87, 87, 87, 47, 47, 22, 7, 7, 7, 7, 7, 4, 4, 4, 4, 1, 1, 7, 22, 22, 22, 22, 47, 71, 71, 87, 87, 22, 22] 97 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 333 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113558 none CCC(C)N1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 85, 95, 85, 85, 85, 85, 46, 46, 46, 25, 25, 25, 9, 9, 9, 5, 2, 1, 1, 1, 1, 1, 1, 9, 9, 25, 95, 95, 95, 95, 95, 95, 95, 95, 95, 85, 85, 46, 25, 25, 25, 25, 9, 5, 5, 2, 2, 25, 25] 95 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 268 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113558 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113558 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113558/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113558/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113558 Building REAL300020113559 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113559' /scratch/stefan/7770410/working/building/REAL300020113559 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113559 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113559/0 /scratch/stefan/7770410/working/building/REAL300020113559 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/727 `/scratch/stefan/7770410/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113559.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113559 none CC(C)CN1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 14, 14, 14, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 48, 53, 53, 53, 53, 11, 11, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 14, 14, 6, 1, 1, 1, 1, 11, 33, 33, 48, 48, 1, 1] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 270 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113559 none CC(C)CN1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 65, 65, 65, 65, 65, 32, 32, 32, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 100, 100, 100, 100, 100, 100, 100, 100, 100, 65, 65, 32, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 376 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113559 none CC(C)CN1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 65, 65, 65, 130, 175, 179, 179, 179, 179, 65, 65, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 5, 14, 14, 14, 14, 65, 130, 130, 175, 175, 14, 14] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 38, 37] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 701 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113559 none CC(C)CN1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 180, 180, 180, 180, 180, 103, 103, 103, 54, 54, 54, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 54, 201, 201, 201, 201, 201, 201, 201, 201, 201, 180, 180, 103, 54, 54, 54, 54, 11, 6, 6, 4, 4, 54, 54] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 545 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113559 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113559/1 /scratch/stefan/7770410/working/building/REAL300020113559 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 728) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/728 `/scratch/stefan/7770410/working/3D/728' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113559.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113559 none CC(C)CN1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 14, 14, 14, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 48, 53, 53, 53, 53, 11, 11, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 14, 14, 6, 1, 1, 1, 1, 11, 33, 33, 48, 48, 1, 1] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 270 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113559 none CC(C)CN1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 65, 65, 65, 65, 65, 32, 32, 32, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 99, 99, 99, 99, 99, 99, 99, 99, 99, 65, 65, 32, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 370 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113559 none CC(C)CN1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 65, 65, 65, 131, 176, 180, 180, 180, 180, 65, 65, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 5, 14, 14, 14, 14, 65, 131, 131, 176, 176, 14, 14] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 38, 37] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 707 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113559 none CC(C)CN1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 181, 181, 181, 181, 181, 104, 104, 104, 55, 55, 55, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 55, 201, 201, 201, 201, 201, 201, 201, 201, 201, 181, 181, 104, 55, 55, 55, 55, 12, 6, 6, 4, 4, 55, 55] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 541 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113559 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113559 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113559/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113559/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113559 Building REAL300020113560 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113560' /scratch/stefan/7770410/working/building/REAL300020113560 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113560 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113560/0 /scratch/stefan/7770410/working/building/REAL300020113560 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 729) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/729 `/scratch/stefan/7770410/working/3D/729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1C1CCCC1) `REAL300020113560.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113560 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 31, 68, 68, 68, 68, 68, 117, 117, 117, 117, 31, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 68, 68, 117, 117, 117, 117, 117, 117, 117, 117, 117] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 351 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113560 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 10, 10, 34, 34, 34, 117, 117, 117, 174, 201, 201, 201, 201, 201, 117, 117, 34, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 10, 34, 34, 34, 34, 117, 174, 174, 201, 201, 34, 34, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 672 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113560 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 50, 50, 50, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 50, 106, 186, 186, 186, 186, 186, 201, 201, 201, 201, 106, 50, 50, 50, 50, 10, 6, 6, 4, 4, 50, 50, 186, 186, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 509 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113560 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 47, 50, 50, 50, 50, 11, 11, 1, 6, 15, 15, 15, 15, 15, 34, 34, 34, 34, 6, 1, 1, 1, 1, 11, 33, 33, 47, 47, 1, 1, 15, 15, 34, 34, 34, 34, 34, 34, 34, 34, 34] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113560 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NN1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 15, 15, 15, 68, 68, 68, 143, 181, 187, 187, 187, 187, 68, 68, 15, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 4, 15, 15, 15, 15, 68, 143, 143, 181, 181, 15, 15, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5] 201 rigid atoms, others: [1, 41, 42, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 706 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113560 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113560/1 /scratch/stefan/7770410/working/building/REAL300020113560 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 730) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/730 `/scratch/stefan/7770410/working/3D/730' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1C1CCCC1) `REAL300020113560.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113560/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113560 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 31, 68, 68, 68, 68, 68, 117, 117, 117, 117, 31, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 68, 68, 117, 117, 117, 117, 117, 117, 117, 117, 117] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 351 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113560 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 10, 10, 34, 34, 34, 117, 117, 117, 174, 201, 201, 201, 201, 201, 117, 117, 34, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 10, 34, 34, 34, 34, 117, 174, 174, 201, 201, 34, 34, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 672 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113560 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 50, 50, 50, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 50, 106, 187, 187, 187, 187, 187, 201, 201, 201, 201, 106, 50, 50, 50, 50, 10, 6, 6, 4, 4, 50, 50, 187, 187, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 507 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113560 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 47, 50, 50, 50, 50, 11, 11, 1, 6, 15, 15, 15, 15, 15, 34, 34, 34, 34, 6, 1, 1, 1, 1, 11, 33, 33, 47, 47, 1, 1, 15, 15, 34, 34, 34, 34, 34, 34, 34, 34, 34] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113560 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NN1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 15, 15, 15, 68, 68, 68, 143, 181, 187, 187, 187, 187, 68, 68, 15, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 4, 15, 15, 15, 15, 68, 143, 143, 181, 181, 15, 15, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5] 201 rigid atoms, others: [1, 41, 42, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 706 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113560 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113560 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113560/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113560/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113560 Building REAL300020113561 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113561' /scratch/stefan/7770410/working/building/REAL300020113561 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113561 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113561/0 /scratch/stefan/7770410/working/building/REAL300020113561 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/731 `/scratch/stefan/7770410/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=CC(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1) `REAL300020113561.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113561 none CN1C=CC(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 23, 21, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 29, 43, 44, 44, 44, 44, 10, 10, 1, 32, 32, 32, 32, 32, 32, 23, 23, 21, 21, 6, 1, 1, 1, 1, 10, 29, 29, 43, 43, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 277 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113561 none CN1C=CC(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 102, 84, 82, 28, 28, 28, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 10, 102, 102, 102, 102, 102, 102, 84, 84, 82, 82, 28, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 373 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113561 none CN1C=CC(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 7, 13, 13, 13, 32, 32, 32, 102, 102, 102, 169, 201, 201, 201, 201, 201, 102, 102, 32, 1, 2, 2, 2, 1, 1, 5, 5, 7, 7, 13, 32, 32, 32, 32, 102, 169, 169, 201, 201, 32, 32] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 748 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113561 none CN1C=CC(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 199, 85, 85, 85, 41, 41, 41, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 41, 201, 201, 201, 201, 201, 201, 201, 201, 199, 199, 85, 41, 41, 41, 41, 9, 5, 5, 3, 3, 41, 41] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 750 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113561 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113561/1 /scratch/stefan/7770410/working/building/REAL300020113561 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 732) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/732 `/scratch/stefan/7770410/working/3D/732' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=CC(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1) `REAL300020113561.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113561 none CN1C=CC(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 23, 21, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 29, 43, 44, 44, 44, 44, 10, 10, 1, 32, 32, 32, 32, 32, 32, 23, 23, 21, 21, 6, 1, 1, 1, 1, 10, 29, 29, 43, 43, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 277 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113561 none CN1C=CC(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 103, 85, 83, 28, 28, 28, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 10, 103, 103, 103, 103, 103, 103, 85, 85, 83, 83, 28, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 376 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113561 none CN1C=CC(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 7, 13, 13, 13, 32, 32, 32, 103, 103, 103, 169, 201, 201, 201, 201, 201, 103, 103, 32, 1, 2, 2, 2, 1, 1, 5, 5, 7, 7, 13, 32, 32, 32, 32, 103, 169, 169, 201, 201, 32, 32] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 743 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113561 none CN1C=CC(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 199, 86, 86, 86, 41, 41, 41, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 41, 201, 201, 201, 201, 201, 201, 201, 201, 199, 199, 86, 41, 41, 41, 41, 9, 5, 5, 3, 3, 41, 41] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 749 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113561 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113561 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113561/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113561/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113561 Building REAL300020113562 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113562' /scratch/stefan/7770410/working/building/REAL300020113562 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113562 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113562/0 /scratch/stefan/7770410/working/building/REAL300020113562 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 733) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/733 `/scratch/stefan/7770410/working/3D/733' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC=C1CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113562.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113562 none CN1N=CC=C1CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 32, 23, 23, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 21, 33, 33, 33, 33, 33, 8, 8, 1, 32, 32, 32, 32, 32, 23, 23, 23, 23, 5, 1, 1, 1, 1, 8, 21, 21, 33, 33, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 232 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113562 none CN1N=CC=C1CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 107, 83, 83, 16, 16, 16, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 107, 107, 107, 107, 107, 83, 83, 83, 83, 16, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 366 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113562 none CN1N=CC=C1CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 19, 19, 19, 32, 32, 32, 107, 107, 107, 155, 201, 201, 201, 201, 201, 107, 107, 32, 2, 2, 2, 1, 1, 3, 3, 3, 3, 19, 32, 32, 32, 32, 107, 155, 155, 201, 201, 32, 32] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 731 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113562 none CN1N=CC=C1CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 169, 169, 49, 49, 49, 33, 33, 33, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 33, 201, 201, 201, 201, 201, 169, 169, 169, 169, 49, 33, 33, 33, 33, 7, 4, 4, 2, 2, 33, 33] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 700 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113562 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113562/1 /scratch/stefan/7770410/working/building/REAL300020113562 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 734) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/734 `/scratch/stefan/7770410/working/3D/734' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC=C1CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113562.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113562 none CN1N=CC=C1CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 32, 23, 23, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 21, 33, 33, 33, 33, 33, 8, 8, 1, 32, 32, 32, 32, 32, 23, 23, 23, 23, 5, 1, 1, 1, 1, 8, 21, 21, 33, 33, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 232 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113562 none CN1N=CC=C1CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 108, 108, 84, 84, 16, 16, 16, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 108, 108, 108, 108, 108, 84, 84, 84, 84, 16, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 369 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113562 none CN1N=CC=C1CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 19, 19, 19, 32, 32, 32, 108, 108, 108, 156, 201, 201, 201, 201, 201, 108, 108, 32, 2, 2, 2, 1, 1, 3, 3, 3, 3, 19, 32, 32, 32, 32, 108, 156, 156, 201, 201, 32, 32] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 726 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113562 none CN1N=CC=C1CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 169, 169, 49, 49, 49, 33, 33, 33, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 33, 201, 201, 201, 201, 201, 169, 169, 169, 169, 49, 33, 33, 33, 33, 7, 4, 4, 2, 2, 33, 33] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 700 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113562 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113562 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113562/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113562/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113562 Building REAL300020113563 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113563' /scratch/stefan/7770410/working/building/REAL300020113563 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113563 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113563/0 /scratch/stefan/7770410/working/building/REAL300020113563 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/735 `/scratch/stefan/7770410/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C2CC2)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113563.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113563 none CN1N=C(C2CC2)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 9, 9, 9, 17, 17, 17, 43, 43, 43, 121, 121, 121, 171, 201, 201, 201, 201, 201, 121, 121, 43, 9, 9, 9, 1, 1, 1, 1, 1, 9, 17, 43, 43, 43, 43, 121, 171, 171, 201, 201, 43, 43] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 35, 31] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 672 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113563 none CN1N=C(C2CC2)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [172, 172, 172, 172, 172, 201, 201, 172, 145, 145, 145, 59, 59, 59, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 59, 172, 172, 172, 201, 201, 201, 201, 201, 172, 145, 59, 59, 59, 59, 11, 6, 6, 4, 4, 59, 59] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 569 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113563 none CN1N=C(C2CC2)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 12, 43, 43, 12, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 35, 50, 60, 60, 60, 60, 11, 11, 1, 12, 12, 12, 43, 43, 43, 43, 43, 12, 6, 1, 1, 1, 1, 11, 35, 35, 50, 50, 1, 1] 201 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 320 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113563 none CN1N=C(C2CC2)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 1, 1, 1, 4, 4, 4, 12, 12, 12, 57, 57, 57, 121, 162, 172, 172, 172, 172, 57, 57, 12, 2, 2, 2, 9, 9, 9, 9, 9, 1, 4, 12, 12, 12, 12, 57, 121, 121, 162, 162, 12, 12] 201 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 36] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 666 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113563 none CN1N=C(C2CC2)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 57, 57, 121, 121, 57, 36, 36, 36, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 57, 57, 57, 121, 121, 121, 121, 121, 57, 36, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 351 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113563 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113563/1 /scratch/stefan/7770410/working/building/REAL300020113563 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 736) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/736 `/scratch/stefan/7770410/working/3D/736' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C2CC2)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113563.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113563/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113563 none CN1N=C(C2CC2)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 9, 9, 9, 17, 17, 17, 41, 41, 41, 123, 123, 123, 171, 201, 201, 201, 201, 201, 123, 123, 41, 9, 9, 9, 1, 1, 1, 1, 1, 9, 17, 41, 41, 41, 41, 123, 171, 171, 201, 201, 41, 41] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 35, 31] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 661 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113563 none CN1N=C(C2CC2)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [172, 172, 172, 172, 172, 201, 201, 172, 145, 145, 145, 59, 59, 59, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 59, 172, 172, 172, 201, 201, 201, 201, 201, 172, 145, 59, 59, 59, 59, 11, 6, 6, 4, 4, 59, 59] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 569 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113563 none CN1N=C(C2CC2)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 12, 41, 41, 12, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 34, 49, 59, 59, 59, 59, 11, 11, 1, 12, 12, 12, 41, 41, 41, 41, 41, 12, 6, 1, 1, 1, 1, 11, 34, 34, 49, 49, 1, 1] 201 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 311 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113563 none CN1N=C(C2CC2)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 1, 1, 1, 4, 4, 4, 12, 12, 12, 57, 57, 57, 121, 162, 172, 172, 172, 172, 57, 57, 12, 2, 2, 2, 9, 9, 9, 9, 9, 1, 4, 12, 12, 12, 12, 57, 121, 121, 162, 162, 12, 12] 201 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 36] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 666 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113563 none CN1N=C(C2CC2)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 57, 57, 123, 123, 57, 36, 36, 36, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 57, 57, 57, 123, 123, 123, 123, 123, 57, 36, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 360 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113563 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113563 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113563/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113563/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113563 Building REAL300020113564 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113564' /scratch/stefan/7770410/working/building/REAL300020113564 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113564 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113564/0 /scratch/stefan/7770410/working/building/REAL300020113564 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/737 `/scratch/stefan/7770410/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=C(C=CO2)N1) `REAL300020113564.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113564 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=C(C=CO2)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 6, 10, 10, 10, 10, 10, 1, 1, 5, 14, 25, 25, 25, 25, 25, 25, 25, 14, 5, 5, 5, 5, 1, 6, 6, 10, 10, 5, 5, 25, 25, 25, 25] 39 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 98 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113564 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=C(C=CO2)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 23, 23, 23, 10, 10, 10, 4, 2, 1, 1, 1, 1, 1, 1, 10, 10, 23, 31, 39, 39, 39, 39, 39, 39, 39, 31, 23, 23, 23, 23, 10, 4, 4, 2, 2, 23, 23, 39, 39, 39, 39] 39 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 103 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113564 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=C(C=CO2)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 14, 23, 23, 23, 23, 23, 5, 5, 1, 6, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 5, 14, 14, 23, 23, 1, 1, 15, 15, 15, 15] 39 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113564 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=C(C=CO2)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 15, 15, 15, 25, 25, 25, 35, 39, 39, 39, 39, 39, 25, 25, 15, 1, 1, 1, 1, 1, 1, 1, 1, 9, 15, 15, 15, 15, 25, 35, 35, 39, 39, 15, 15, 1, 1, 1, 1] 39 rigid atoms, others: [1, 39, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 127 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113564 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113564/1 /scratch/stefan/7770410/working/building/REAL300020113564 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 738) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/738 `/scratch/stefan/7770410/working/3D/738' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=C(C=CO2)N1) `REAL300020113564.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113564/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113564 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=C(C=CO2)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 6, 10, 10, 10, 10, 10, 1, 1, 5, 14, 25, 25, 25, 25, 25, 25, 25, 14, 5, 5, 5, 5, 1, 6, 6, 10, 10, 5, 5, 25, 25, 25, 25] 39 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 98 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113564 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=C(C=CO2)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 23, 23, 23, 10, 10, 10, 4, 2, 1, 1, 1, 1, 1, 1, 10, 10, 23, 31, 39, 39, 39, 39, 39, 39, 39, 31, 23, 23, 23, 23, 10, 4, 4, 2, 2, 23, 23, 39, 39, 39, 39] 39 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 103 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113564 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=C(C=CO2)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 14, 23, 23, 23, 23, 23, 5, 5, 1, 6, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 5, 14, 14, 23, 23, 1, 1, 15, 15, 15, 15] 39 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113564 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=C(C=CO2)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 15, 15, 15, 25, 25, 25, 35, 39, 39, 39, 39, 39, 25, 25, 15, 1, 1, 1, 1, 1, 1, 1, 1, 9, 15, 15, 15, 15, 25, 35, 35, 39, 39, 15, 15, 1, 1, 1, 1] 39 rigid atoms, others: [1, 39, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 127 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113564 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113564 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113564/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113564/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113564 Building REAL300020113565 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113565' /scratch/stefan/7770410/working/building/REAL300020113565 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113565 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113565/0 /scratch/stefan/7770410/working/building/REAL300020113565 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/739 `/scratch/stefan/7770410/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NS1) `REAL300020113565.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113565 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 7, 9, 9, 9, 9, 9, 1, 1, 5, 12, 24, 24, 24, 24, 12, 5, 5, 5, 5, 1, 7, 7, 9, 9, 5, 5, 24, 24] 41 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 29] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113565 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 21, 21, 21, 10, 10, 10, 5, 2, 1, 1, 1, 1, 1, 1, 10, 10, 21, 29, 41, 41, 41, 41, 29, 21, 21, 21, 21, 10, 5, 5, 2, 2, 21, 21, 41, 41] 41 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 113 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113565 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 14, 20, 20, 20, 20, 20, 5, 5, 1, 6, 16, 16, 16, 16, 6, 1, 1, 1, 1, 5, 14, 14, 20, 20, 1, 1, 16, 16] 41 rigid atoms, others: [2, 3, 4, 5, 6, 34, 18, 35, 25, 26, 27, 28] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113565 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 16, 16, 16, 24, 24, 24, 36, 41, 41, 41, 41, 41, 24, 24, 16, 1, 1, 1, 1, 1, 7, 16, 16, 16, 16, 24, 36, 36, 41, 41, 16, 16, 1, 1] 41 rigid atoms, others: [1, 36, 37, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 146 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113565 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113565/1 /scratch/stefan/7770410/working/building/REAL300020113565 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 740) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/740 `/scratch/stefan/7770410/working/3D/740' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NS1) `REAL300020113565.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113565 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 7, 9, 9, 9, 9, 9, 1, 1, 5, 13, 25, 25, 25, 25, 13, 5, 5, 5, 5, 1, 7, 7, 9, 9, 5, 5, 25, 25] 42 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 29] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 89 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113565 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 22, 22, 22, 10, 10, 10, 5, 2, 1, 1, 1, 1, 1, 1, 10, 10, 22, 30, 42, 42, 42, 42, 30, 22, 22, 22, 22, 10, 5, 5, 2, 2, 22, 22, 42, 42] 42 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 115 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113565 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 14, 21, 21, 21, 21, 21, 5, 5, 1, 6, 16, 16, 16, 16, 6, 1, 1, 1, 1, 5, 14, 14, 21, 21, 1, 1, 16, 16] 42 rigid atoms, others: [2, 3, 4, 5, 6, 34, 18, 35, 25, 26, 27, 28] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113565 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 16, 16, 16, 25, 25, 25, 37, 42, 42, 42, 42, 42, 25, 25, 16, 1, 1, 1, 1, 1, 7, 16, 16, 16, 16, 25, 37, 37, 42, 42, 16, 16, 1, 1] 42 rigid atoms, others: [1, 36, 37, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 148 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113565 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113565 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113565/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113565/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113565 Building REAL300020113566 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113566' /scratch/stefan/7770410/working/building/REAL300020113566 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113566 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113566/0 /scratch/stefan/7770410/working/building/REAL300020113566 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 741) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/741 `/scratch/stefan/7770410/working/3D/741' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)C(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)OCC) `REAL300020113566.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113566 none C=C(C)C(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)OCC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [112, 81, 112, 55, 33, 33, 33, 9, 9, 9, 1, 1, 1, 1, 1, 8, 8, 12, 12, 12, 12, 1, 1, 9, 81, 111, 117, 112, 112, 112, 112, 112, 81, 55, 55, 33, 9, 9, 9, 9, 1, 8, 8, 8, 8, 9, 9, 117, 117, 117, 117, 117] 180 rigid atoms, others: [40, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 595 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113566 none C=C(C)C(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)OCC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [120, 108, 120, 94, 77, 77, 77, 34, 34, 34, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 9, 9, 34, 108, 120, 120, 120, 120, 120, 120, 120, 108, 94, 94, 77, 34, 34, 34, 34, 9, 4, 4, 4, 4, 34, 34, 120, 120, 120, 120, 120] 120 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 453 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113566 none C=C(C)C(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)OCC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [45, 21, 45, 12, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 37, 37, 49, 49, 49, 49, 9, 9, 1, 21, 35, 43, 45, 45, 45, 45, 45, 21, 12, 12, 6, 1, 1, 1, 1, 9, 37, 37, 37, 37, 1, 1, 43, 43, 43, 43, 43] 180 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 45, 46, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51]) total number of confs: 387 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113566 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113566/1 /scratch/stefan/7770410/working/building/REAL300020113566 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 742) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/742 `/scratch/stefan/7770410/working/3D/742' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)C(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)OCC) `REAL300020113566.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113566 none C=C(C)C(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)OCC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [113, 81, 113, 56, 33, 33, 33, 9, 9, 9, 1, 1, 1, 1, 1, 8, 8, 12, 12, 12, 12, 1, 1, 9, 81, 111, 117, 113, 113, 113, 113, 113, 81, 56, 56, 33, 9, 9, 9, 9, 1, 8, 8, 8, 8, 9, 9, 117, 117, 117, 117, 117] 181 rigid atoms, others: [40, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 597 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113566 none C=C(C)C(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)OCC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [119, 110, 119, 94, 78, 78, 78, 35, 35, 35, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 9, 9, 35, 110, 119, 119, 119, 119, 119, 119, 119, 110, 94, 94, 78, 35, 35, 35, 35, 9, 4, 4, 4, 4, 35, 35, 119, 119, 119, 119, 119] 119 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 443 number of broken/clashed sets: 9 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113566 none C=C(C)C(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)OCC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [45, 21, 45, 12, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 37, 37, 50, 50, 50, 50, 9, 9, 1, 21, 35, 43, 45, 45, 45, 45, 45, 21, 12, 12, 6, 1, 1, 1, 1, 9, 37, 37, 37, 37, 1, 1, 43, 43, 43, 43, 43] 181 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 45, 46, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51]) total number of confs: 389 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113566 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113566 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113566/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113566/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113566 Building REAL300020113567 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113567' /scratch/stefan/7770410/working/building/REAL300020113567 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113567 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113567/0 /scratch/stefan/7770410/working/building/REAL300020113567 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/743 `/scratch/stefan/7770410/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CC(F)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113567.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113567 none CC[NH+](CC)CC(F)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 96, 47, 96, 96, 116, 31, 15, 31, 15, 15, 8, 8, 8, 1, 1, 1, 1, 1, 7, 9, 14, 14, 14, 14, 1, 1, 8, 114, 114, 114, 114, 114, 116, 116, 116, 116, 116, 47, 47, 31, 15, 8, 8, 8, 8, 1, 7, 7, 9, 9, 8, 8] 201 rigid atoms, others: [46, 15, 16, 17, 18, 14, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 724 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113567 none CC[NH+](CC)CC(F)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [91, 80, 68, 80, 80, 91, 48, 25, 48, 25, 25, 19, 19, 19, 9, 9, 9, 5, 2, 1, 1, 1, 1, 1, 1, 9, 9, 19, 91, 91, 91, 91, 91, 91, 91, 91, 91, 91, 68, 68, 48, 25, 19, 19, 19, 19, 9, 5, 5, 2, 2, 19, 19] 91 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 516 number of broken/clashed sets: 91 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113567 none CC[NH+](CC)CC(F)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 45, 22, 45, 45, 61, 14, 5, 14, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 34, 39, 51, 51, 51, 51, 8, 8, 1, 60, 60, 60, 60, 60, 61, 61, 61, 61, 61, 22, 22, 14, 5, 1, 1, 1, 1, 8, 34, 34, 39, 39, 1, 1] 201 rigid atoms, others: [45, 43, 44, 42, 11, 12, 13, 14, 15, 51, 52, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50]) total number of confs: 559 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113567 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113567/1 /scratch/stefan/7770410/working/building/REAL300020113567 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 744) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/744 `/scratch/stefan/7770410/working/3D/744' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CC(F)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113567.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113567/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113567 none CCN(CC)CC(F)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [122, 98, 66, 98, 127, 54, 27, 54, 27, 27, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 122, 122, 122, 122, 122, 127, 127, 127, 127, 127, 66, 66, 54, 27, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [45, 14, 13, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 696 number of broken/clashed sets: 89 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113567 none CCN(CC)CC(F)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 182, 154, 182, 201, 119, 72, 119, 72, 72, 54, 54, 54, 19, 19, 19, 6, 4, 1, 1, 1, 1, 1, 1, 19, 19, 54, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 154, 154, 119, 72, 54, 54, 54, 54, 19, 6, 6, 4, 4, 54, 54] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 966 number of broken/clashed sets: 76 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113567 none CCN(CC)CC(F)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 51, 29, 51, 71, 21, 6, 21, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 29, 31, 34, 34, 34, 34, 9, 9, 1, 67, 67, 67, 67, 67, 71, 71, 71, 71, 71, 29, 29, 21, 6, 1, 1, 1, 1, 9, 29, 29, 31, 31, 1, 1] 201 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 44, 50, 51, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 487 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113567 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113567 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113567/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113567/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113567 Building REAL300020113568 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113568' /scratch/stefan/7770410/working/building/REAL300020113568 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113568 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113568/0 /scratch/stefan/7770410/working/building/REAL300020113568 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/745 `/scratch/stefan/7770410/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1) `REAL300020113568.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113568 none CCC1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 17, 17, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 40, 59, 69, 69, 69, 69, 13, 13, 1, 17, 27, 27, 27, 27, 27, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 13, 40, 40, 59, 59, 1, 1] 201 rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 47, 48, 40, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 363 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113568 none CCC1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 87, 87, 87, 87, 53, 53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 87, 113, 113, 113, 113, 113, 87, 87, 87, 87, 87, 87, 53, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [42, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 443 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113568 none CCC1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 17, 17, 17, 87, 87, 87, 166, 197, 201, 201, 201, 201, 87, 87, 17, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 8, 17, 17, 17, 17, 87, 166, 166, 197, 197, 17, 17] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 34, 35, 25, 36, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 700 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113568 none CCC1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 182, 182, 182, 69, 69, 69, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 69, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 182, 69, 69, 69, 69, 10, 6, 6, 4, 4, 69, 69] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 577 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113568 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113568/1 /scratch/stefan/7770410/working/building/REAL300020113568 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 746) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/746 `/scratch/stefan/7770410/working/3D/746' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1) `REAL300020113568.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113568/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113568 none CCC1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 17, 17, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 41, 60, 70, 70, 70, 70, 13, 13, 1, 17, 27, 27, 27, 27, 27, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 13, 41, 41, 60, 60, 1, 1] 201 rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 47, 48, 40, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 366 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113568 none CCC1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 86, 86, 86, 86, 53, 53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 86, 113, 113, 113, 113, 113, 86, 86, 86, 86, 86, 86, 53, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [42, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 445 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113568 none CCC1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 17, 17, 17, 86, 86, 86, 167, 197, 201, 201, 201, 201, 86, 86, 17, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 8, 17, 17, 17, 17, 86, 167, 167, 197, 197, 17, 17] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 34, 35, 25, 36, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 702 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113568 none CCC1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 183, 183, 183, 71, 71, 71, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 71, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 183, 71, 71, 71, 71, 11, 6, 6, 4, 4, 71, 71] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 573 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113568 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113568 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113568/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113568/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113568 Building REAL300020113569 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113569' /scratch/stefan/7770410/working/building/REAL300020113569 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113569 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113569/0 /scratch/stefan/7770410/working/building/REAL300020113569 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/747 `/scratch/stefan/7770410/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN2CCCCC2=N1) `REAL300020113569.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113569 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN2CCCCC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 20, 20, 20, 20, 1, 1, 13, 55, 92, 92, 92, 92, 92, 92, 92, 92, 55, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 92, 92, 92, 92, 92, 92, 92, 92, 92] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 262 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113569 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN2CCCCC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [192, 192, 117, 117, 117, 23, 23, 23, 6, 4, 1, 1, 1, 1, 1, 1, 23, 23, 117, 192, 201, 201, 201, 201, 201, 201, 201, 201, 192, 117, 117, 117, 117, 23, 6, 6, 4, 4, 117, 117, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 536 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113569 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN2CCCCC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 68, 92, 116, 116, 116, 116, 13, 13, 1, 6, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 13, 68, 68, 92, 92, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 434 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113569 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN2CCCCC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 19, 19, 19, 92, 92, 92, 172, 201, 201, 201, 201, 201, 92, 92, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 19, 92, 172, 172, 201, 201, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 681 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113569 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113569/1 /scratch/stefan/7770410/working/building/REAL300020113569 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 748) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/748 `/scratch/stefan/7770410/working/3D/748' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN2CCCCC2=N1) `REAL300020113569.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113569/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113569 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN2CCCCC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 20, 20, 20, 20, 1, 1, 13, 55, 92, 92, 92, 92, 92, 92, 92, 92, 55, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 92, 92, 92, 92, 92, 92, 92, 92, 92] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 264 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113569 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN2CCCCC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [194, 194, 115, 115, 115, 22, 22, 22, 6, 4, 1, 1, 1, 1, 1, 1, 22, 22, 115, 194, 201, 201, 201, 201, 201, 201, 201, 201, 194, 115, 115, 115, 115, 22, 6, 6, 4, 4, 115, 115, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 546 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113569 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN2CCCCC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 67, 90, 114, 114, 114, 114, 13, 13, 1, 6, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 13, 67, 67, 90, 90, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 426 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113569 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN2CCCCC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 20, 20, 20, 92, 92, 92, 170, 201, 201, 201, 201, 201, 92, 92, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 20, 20, 20, 20, 92, 170, 170, 201, 201, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 686 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113569 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113569 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113569/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113569/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113569 Building REAL300020113570 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113570' /scratch/stefan/7770410/working/building/REAL300020113570 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113570 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113570/0 /scratch/stefan/7770410/working/building/REAL300020113570 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/749 `/scratch/stefan/7770410/working/3D/749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(Cl)=NN1) `REAL300020113570.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113570 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(Cl)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'Cl', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 16, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 30, 46, 52, 52, 52, 52, 9, 9, 1, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 9, 30, 30, 46, 46, 1, 1, 17] 201 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 39, 40, 21, 30, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41]) total number of confs: 233 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113570 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(Cl)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'Cl', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 16, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 34, 34, 34, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 83, 83, 83, 83, 83, 83, 83, 34, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9, 83] 201 rigid atoms, others: [34, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 193 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113570 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(Cl)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'Cl', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 16, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 17, 17, 17, 83, 83, 83, 150, 201, 201, 201, 201, 201, 83, 83, 17, 1, 1, 1, 1, 2, 2, 2, 7, 17, 17, 17, 17, 83, 150, 150, 201, 201, 17, 17, 1] 201 rigid atoms, others: [0, 1, 2, 3, 41, 22, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 783 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113570 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(Cl)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'Cl', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 16, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 88, 88, 88, 52, 52, 52, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 52, 201, 201, 201, 201, 201, 201, 201, 88, 52, 52, 52, 52, 11, 6, 6, 4, 4, 52, 52, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 422 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113570 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113570/1 /scratch/stefan/7770410/working/building/REAL300020113570 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 750) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/750 `/scratch/stefan/7770410/working/3D/750' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(Cl)=NN1) `REAL300020113570.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113570/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113570 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(Cl)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'Cl', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 16, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 29, 45, 52, 52, 52, 52, 9, 9, 1, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 9, 29, 29, 45, 45, 1, 1, 17] 201 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 39, 40, 21, 30, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41]) total number of confs: 232 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113570 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(Cl)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'Cl', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 16, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 34, 34, 34, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 83, 83, 83, 83, 83, 83, 83, 34, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 83] 201 rigid atoms, others: [34, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 190 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113570 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(Cl)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'Cl', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 16, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 17, 17, 17, 83, 83, 83, 149, 201, 201, 201, 201, 201, 83, 83, 17, 1, 1, 1, 1, 2, 2, 2, 7, 17, 17, 17, 17, 83, 149, 149, 201, 201, 17, 17, 1] 201 rigid atoms, others: [0, 1, 2, 3, 41, 22, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 786 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113570 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(Cl)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'Cl', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 16, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 88, 88, 88, 52, 52, 52, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 52, 201, 201, 201, 201, 201, 201, 201, 88, 52, 52, 52, 52, 11, 6, 6, 4, 4, 52, 52, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 422 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113570 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113570 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113570/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113570/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113570 Building REAL300020113571 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113571' /scratch/stefan/7770410/working/building/REAL300020113571 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113571 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113571/0 /scratch/stefan/7770410/working/building/REAL300020113571 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/751 `/scratch/stefan/7770410/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1C=CC(C(F)F)=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113571.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113571 none O=C(CN1C=CC(C(F)F)=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 5, 15, 15, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 24, 30, 30, 30, 30, 58, 58, 30, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 38, 38, 38, 38, 8, 8, 1, 24, 24, 30, 30, 58, 6, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 44, 11, 12, 13, 14, 15, 43, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 381 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113571 none O=C(CN1C=CC(C(F)F)=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 5, 15, 15, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 74, 83, 83, 83, 83, 125, 125, 83, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 8, 74, 74, 83, 83, 125, 24, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [38, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 542 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113571 none O=C(CN1C=CC(C(F)F)=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 5, 15, 15, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 7, 1, 1, 1, 1, 1, 1, 6, 6, 1, 14, 14, 30, 30, 30, 83, 83, 83, 151, 198, 201, 201, 201, 201, 83, 83, 30, 7, 7, 1, 1, 6, 14, 30, 30, 30, 30, 83, 151, 151, 198, 198, 30, 30] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 10, 30, 31] set([0, 1, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 789 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113571 none O=C(CN1C=CC(C(F)F)=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 5, 15, 15, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 196, 201, 201, 201, 201, 201, 201, 201, 39, 39, 39, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 39, 196, 196, 201, 201, 201, 81, 39, 39, 39, 39, 10, 6, 6, 4, 4, 39, 39] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 728 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113571 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113571/1 /scratch/stefan/7770410/working/building/REAL300020113571 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 752) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/752 `/scratch/stefan/7770410/working/3D/752' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1C=CC(C(F)F)=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113571.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113571 none O=C(CN1C=CC(C(F)F)=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 5, 15, 15, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 24, 30, 30, 30, 30, 58, 58, 30, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 38, 38, 38, 38, 8, 8, 1, 24, 24, 30, 30, 58, 6, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 44, 11, 12, 13, 14, 15, 43, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 381 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113571 none O=C(CN1C=CC(C(F)F)=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 5, 15, 15, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 74, 83, 83, 83, 83, 125, 125, 83, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 8, 74, 74, 83, 83, 125, 24, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [38, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 542 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113571 none O=C(CN1C=CC(C(F)F)=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 5, 15, 15, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 7, 1, 1, 1, 1, 1, 1, 6, 6, 1, 14, 14, 30, 30, 30, 83, 83, 83, 151, 198, 201, 201, 201, 201, 83, 83, 30, 7, 7, 1, 1, 6, 14, 30, 30, 30, 30, 83, 151, 151, 198, 198, 30, 30] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 10, 30, 31] set([0, 1, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 789 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113571 none O=C(CN1C=CC(C(F)F)=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 5, 15, 15, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 196, 201, 201, 201, 201, 201, 201, 201, 38, 38, 38, 9, 9, 9, 6, 4, 1, 1, 1, 1, 1, 1, 9, 9, 38, 196, 196, 201, 201, 201, 81, 38, 38, 38, 38, 9, 6, 6, 4, 4, 38, 38] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 728 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113571 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113571 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113571/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113571/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113571 Building REAL300020113572 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113572' /scratch/stefan/7770410/working/building/REAL300020113572 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113572 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113572/0 /scratch/stefan/7770410/working/building/REAL300020113572 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/753 `/scratch/stefan/7770410/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1) `REAL300020113572.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113572 none COCCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 32, 23, 20, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 28, 42, 43, 43, 43, 43, 10, 10, 1, 20, 20, 41, 41, 41, 32, 32, 23, 23, 6, 1, 1, 1, 1, 10, 28, 28, 42, 42, 1, 1, 20, 20, 20, 20] 201 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48]) total number of confs: 318 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113572 none COCCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 106, 88, 84, 34, 34, 34, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 10, 84, 84, 115, 115, 115, 106, 106, 88, 88, 34, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 84, 84, 84, 84] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 413 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113572 none COCCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 4, 1, 1, 1, 5, 5, 5, 20, 20, 20, 84, 84, 84, 146, 185, 185, 185, 185, 185, 84, 84, 20, 1, 1, 11, 11, 11, 6, 6, 4, 4, 5, 20, 20, 20, 20, 84, 146, 146, 185, 185, 20, 20, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 45, 46, 47, 48, 24, 25] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 722 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113572 none COCCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 198, 198, 110, 110, 110, 46, 46, 46, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 46, 198, 198, 201, 201, 201, 201, 201, 198, 198, 110, 46, 46, 46, 46, 10, 6, 6, 4, 4, 46, 46, 198, 198, 198, 198] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 583 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113572 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113572/1 /scratch/stefan/7770410/working/building/REAL300020113572 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 754) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/754 `/scratch/stefan/7770410/working/3D/754' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1) `REAL300020113572.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113572/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113572 none COCCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 32, 23, 20, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 28, 42, 43, 43, 43, 43, 10, 10, 1, 20, 20, 42, 42, 42, 32, 32, 23, 23, 6, 1, 1, 1, 1, 10, 28, 28, 42, 42, 1, 1, 20, 20, 20, 20] 201 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48]) total number of confs: 320 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113572 none COCCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 107, 88, 84, 34, 34, 34, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 10, 84, 84, 116, 116, 116, 107, 107, 88, 88, 34, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 84, 84, 84, 84] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 419 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113572 none COCCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 4, 1, 1, 1, 5, 5, 5, 20, 20, 20, 84, 84, 84, 146, 184, 184, 184, 184, 184, 84, 84, 20, 1, 1, 11, 11, 11, 6, 6, 4, 4, 5, 20, 20, 20, 20, 84, 146, 146, 184, 184, 20, 20, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 45, 46, 47, 48, 24, 25] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 716 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113572 none COCCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 198, 198, 111, 111, 111, 46, 46, 46, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 46, 198, 198, 201, 201, 201, 201, 201, 198, 198, 111, 46, 46, 46, 46, 10, 6, 6, 4, 4, 46, 46, 198, 198, 198, 198] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 585 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113572 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113572 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113572/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113572/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113572 Building REAL300020113573 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113573' /scratch/stefan/7770410/working/building/REAL300020113573 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113573 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113573/0 /scratch/stefan/7770410/working/building/REAL300020113573 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 755) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/755 `/scratch/stefan/7770410/working/3D/755' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1) `REAL300020113573.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113573 none CC(C)CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 31, 47, 47, 47, 47, 47, 10, 10, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 10, 31, 31, 47, 47, 1, 1, 15, 15, 15, 15] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 45, 46, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50]) total number of confs: 234 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113573 none CC(C)CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 80, 41, 41, 41, 10, 10, 10, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 10, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 41, 10, 10, 10, 10, 1, 5, 5, 7, 7, 10, 10, 80, 80, 80, 80] 201 rigid atoms, others: [40, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 270 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113573 none CC(C)CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 1, 1, 1, 4, 4, 4, 15, 15, 15, 80, 80, 80, 170, 201, 201, 201, 201, 201, 80, 80, 15, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 15, 15, 15, 15, 80, 170, 170, 201, 201, 15, 15, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 47, 48, 49, 50, 24, 25] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 744 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113573 none CC(C)CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [136, 136, 136, 136, 69, 69, 69, 38, 38, 38, 12, 12, 12, 8, 4, 1, 1, 1, 1, 1, 1, 12, 12, 38, 136, 136, 136, 136, 136, 136, 136, 136, 136, 136, 136, 69, 38, 38, 38, 38, 12, 8, 8, 4, 4, 38, 38, 136, 136, 136, 136] 136 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 415 number of broken/clashed sets: 22 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113573 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113573/1 /scratch/stefan/7770410/working/building/REAL300020113573 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 756) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/756 `/scratch/stefan/7770410/working/3D/756' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1) `REAL300020113573.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113573 none CC(C)CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 31, 47, 47, 47, 47, 47, 10, 10, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 10, 31, 31, 47, 47, 1, 1, 15, 15, 15, 15] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 45, 46, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50]) total number of confs: 234 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113573 none CC(C)CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 80, 41, 41, 41, 10, 10, 10, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 10, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 41, 10, 10, 10, 10, 1, 5, 5, 7, 7, 10, 10, 80, 80, 80, 80] 201 rigid atoms, others: [40, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 270 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113573 none CC(C)CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 1, 1, 1, 4, 4, 4, 15, 15, 15, 80, 80, 80, 170, 201, 201, 201, 201, 201, 80, 80, 15, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 15, 15, 15, 15, 80, 170, 170, 201, 201, 15, 15, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 47, 48, 49, 50, 24, 25] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 744 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113573 none CC(C)CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 139, 139, 71, 71, 71, 38, 38, 38, 12, 12, 12, 8, 4, 1, 1, 1, 1, 1, 1, 12, 12, 38, 139, 139, 139, 139, 139, 139, 139, 139, 139, 139, 139, 71, 38, 38, 38, 38, 12, 8, 8, 4, 4, 38, 38, 139, 139, 139, 139] 139 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 425 number of broken/clashed sets: 22 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113573 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113573 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113573/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113573/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113573 Building REAL300020113574 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113574' /scratch/stefan/7770410/working/building/REAL300020113574 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113574 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113574/0 /scratch/stefan/7770410/working/building/REAL300020113574 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/757 `/scratch/stefan/7770410/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=NN1C) `REAL300020113574.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113574 none CC1=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 23, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 20, 32, 32, 32, 32, 32, 8, 8, 1, 45, 45, 45, 45, 45, 45, 45, 23, 23, 5, 1, 1, 1, 1, 8, 20, 20, 32, 32, 1, 1, 45, 45, 45, 45] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 246 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113574 none CC1=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 77, 17, 17, 17, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 127, 127, 127, 127, 127, 127, 127, 77, 77, 17, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8, 127, 127, 127, 127] 201 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 383 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113574 none CC1=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 25, 25, 25, 45, 45, 45, 127, 127, 127, 178, 201, 201, 201, 201, 201, 127, 127, 45, 1, 1, 1, 1, 2, 2, 2, 6, 6, 25, 45, 45, 45, 45, 127, 178, 178, 201, 201, 45, 45, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 44, 23, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 666 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113574 none CC1=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 147, 47, 47, 47, 32, 32, 32, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 32, 201, 201, 201, 201, 201, 201, 201, 147, 147, 47, 32, 32, 32, 32, 7, 4, 4, 2, 2, 32, 32, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 646 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113574 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113574/1 /scratch/stefan/7770410/working/building/REAL300020113574 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 758) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/758 `/scratch/stefan/7770410/working/3D/758' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=NN1C) `REAL300020113574.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113574/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113574 none CC1=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 23, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 20, 32, 32, 32, 32, 32, 8, 8, 1, 44, 44, 44, 44, 44, 44, 44, 23, 23, 5, 1, 1, 1, 1, 8, 20, 20, 32, 32, 1, 1, 44, 44, 44, 44] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 244 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113574 none CC1=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 77, 17, 17, 17, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 128, 128, 128, 128, 128, 128, 128, 77, 77, 17, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8, 128, 128, 128, 128] 201 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 385 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113574 none CC1=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 25, 25, 25, 44, 44, 44, 128, 128, 128, 178, 201, 201, 201, 201, 201, 128, 128, 44, 1, 1, 1, 1, 2, 2, 2, 6, 6, 25, 44, 44, 44, 44, 128, 178, 178, 201, 201, 44, 44, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 44, 23, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 655 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113574 none CC1=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 148, 47, 47, 47, 32, 32, 32, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 32, 201, 201, 201, 201, 201, 201, 201, 148, 148, 47, 32, 32, 32, 32, 7, 4, 4, 2, 2, 32, 32, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 644 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113574 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113574 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113574/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113574/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113574 Building REAL300020113575 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113575' /scratch/stefan/7770410/working/building/REAL300020113575 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113575 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113575/0 /scratch/stefan/7770410/working/building/REAL300020113575 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 759) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/759 `/scratch/stefan/7770410/working/3D/759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C2CC2)C=CN1) `REAL300020113575.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113575 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C2CC2)C=CN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 3, 6, 12, 12, 16, 16, 12, 12, 12, 6, 3, 3, 3, 3, 1, 5, 5, 5, 5, 3, 3, 16, 16, 16, 16, 16, 12, 12, 12] 20 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113575 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C2CC2)C=CN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 11, 11, 16, 16, 16, 16, 16, 16, 20, 20, 20, 20, 20, 20, 16, 16, 16, 4, 1, 1, 1, 1, 4, 4, 4, 11, 16, 16, 16, 16, 16, 20, 20, 20, 20, 16, 16, 1, 1, 1, 1, 1, 4, 4, 4] 20 rigid atoms, others: [39, 40, 41, 42, 43, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46]) total number of confs: 69 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113575 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C2CC2)C=CN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 11, 11, 15, 15, 11, 11, 11, 6, 3, 3, 3, 3, 3, 3, 3, 1, 1, 3, 3, 15, 15, 15, 15, 15, 11, 11, 11] 15 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 43 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113575 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C2CC2)C=CN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 3, 3, 1, 5, 12, 12, 16, 16, 12, 12, 12, 5, 1, 1, 1, 1, 3, 5, 5, 5, 5, 1, 1, 16, 16, 16, 16, 16, 12, 12, 12] 20 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113575 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C2CC2)C=CN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 12, 12, 12, 12, 12, 12, 15, 15, 15, 15, 15, 15, 12, 12, 12, 1, 1, 1, 4, 4, 1, 1, 1, 6, 12, 12, 12, 12, 12, 15, 15, 15, 15, 12, 12, 4, 4, 4, 4, 4, 1, 1, 1] 20 rigid atoms, others: [1, 44, 45, 46, 19, 20, 21, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 59 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113575 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113575/1 /scratch/stefan/7770410/working/building/REAL300020113575 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 760) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/760 `/scratch/stefan/7770410/working/3D/760' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C2CC2)C=CN1) `REAL300020113575.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113575/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113575 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C2CC2)C=CN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 3, 6, 13, 13, 17, 17, 13, 13, 13, 6, 3, 3, 3, 3, 1, 5, 5, 5, 5, 3, 3, 17, 17, 17, 17, 17, 13, 13, 13] 21 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113575 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C2CC2)C=CN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 12, 12, 17, 17, 17, 17, 17, 17, 21, 21, 21, 21, 21, 21, 17, 17, 17, 5, 1, 1, 1, 1, 5, 5, 5, 12, 17, 17, 17, 17, 17, 21, 21, 21, 21, 17, 17, 1, 1, 1, 1, 1, 5, 5, 5] 21 rigid atoms, others: [39, 40, 41, 42, 43, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46]) total number of confs: 70 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113575 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C2CC2)C=CN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 12, 12, 16, 16, 12, 12, 12, 6, 3, 3, 3, 3, 3, 3, 3, 1, 1, 3, 3, 16, 16, 16, 16, 16, 12, 12, 12] 16 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 44 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113575 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C2CC2)C=CN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 3, 3, 1, 5, 13, 13, 17, 17, 13, 13, 13, 5, 1, 1, 1, 1, 3, 5, 5, 5, 5, 1, 1, 17, 17, 17, 17, 17, 13, 13, 13] 21 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113575 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C2CC2)C=CN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 13, 13, 13, 13, 13, 13, 16, 16, 16, 16, 16, 16, 13, 13, 13, 1, 1, 1, 5, 5, 1, 1, 1, 7, 13, 13, 13, 13, 13, 16, 16, 16, 16, 13, 13, 5, 5, 5, 5, 5, 1, 1, 1] 21 rigid atoms, others: [1, 44, 45, 46, 19, 20, 21, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 63 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113575 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113575 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113575/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113575/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113575 Building REAL300020113576 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113576' /scratch/stefan/7770410/working/building/REAL300020113576 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113576 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113576/0 /scratch/stefan/7770410/working/building/REAL300020113576 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 761) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/761 `/scratch/stefan/7770410/working/3D/761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1C1CC1) `REAL300020113576.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113576 none CCN1N=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 32, 44, 44, 44, 44, 44, 11, 11, 1, 6, 6, 6, 16, 16, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 11, 32, 32, 44, 44, 1, 1, 6, 16, 16, 16, 16, 16] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 44, 45, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51]) total number of confs: 270 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113576 none CCN1N=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 83, 83, 83, 164, 191, 191, 191, 191, 191, 83, 83, 16, 4, 1, 1, 1, 1, 9, 9, 9, 9, 9, 4, 16, 16, 16, 16, 83, 164, 164, 191, 191, 16, 16, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [47, 48, 49, 50, 51, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 697 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113576 none CCN1N=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 43, 43, 43, 43, 43, 43, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 11, 43, 43, 43, 83, 83, 90, 90, 90, 90, 90, 43, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 43, 83, 83, 83, 83, 83] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 510 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113576 none CCN1N=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 43, 43, 43, 107, 127, 127, 127, 127, 127, 43, 43, 6, 1, 1, 1, 4, 4, 5, 5, 5, 4, 4, 1, 6, 6, 6, 6, 43, 107, 107, 127, 127, 6, 6, 1, 4, 4, 4, 4, 4] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 34, 46, 24, 25, 26] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51]) total number of confs: 486 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113576 none CCN1N=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [195, 127, 127, 127, 127, 127, 127, 44, 44, 44, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 44, 127, 127, 127, 191, 191, 195, 195, 195, 195, 195, 127, 44, 44, 44, 44, 8, 4, 4, 2, 2, 44, 44, 127, 191, 191, 191, 191, 191] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 999 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113576 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113576/1 /scratch/stefan/7770410/working/building/REAL300020113576 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 762) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/762 `/scratch/stefan/7770410/working/3D/762' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1C1CC1) `REAL300020113576.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113576 none CCN1N=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 32, 44, 44, 44, 44, 44, 11, 11, 1, 6, 6, 6, 16, 16, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 11, 32, 32, 44, 44, 1, 1, 6, 16, 16, 16, 16, 16] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 44, 45, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51]) total number of confs: 270 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113576 none CCN1N=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 84, 84, 84, 164, 191, 191, 191, 191, 191, 84, 84, 16, 4, 1, 1, 1, 1, 9, 9, 9, 9, 9, 4, 16, 16, 16, 16, 84, 164, 164, 191, 191, 16, 16, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [47, 48, 49, 50, 51, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 696 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113576 none CCN1N=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 44, 44, 44, 44, 44, 44, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 11, 44, 44, 44, 84, 84, 92, 92, 92, 92, 92, 44, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 44, 84, 84, 84, 84, 84] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 520 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113576 none CCN1N=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 44, 44, 44, 107, 128, 128, 128, 128, 128, 44, 44, 6, 1, 1, 1, 4, 4, 5, 5, 5, 4, 4, 1, 6, 6, 6, 6, 44, 107, 107, 128, 128, 6, 6, 1, 4, 4, 4, 4, 4] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 34, 46, 24, 25, 26] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51]) total number of confs: 487 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113576 none CCN1N=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [195, 127, 127, 127, 127, 127, 127, 44, 44, 44, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 44, 127, 127, 127, 191, 191, 195, 195, 195, 195, 195, 127, 44, 44, 44, 44, 8, 4, 4, 2, 2, 44, 44, 127, 191, 191, 191, 191, 191] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 999 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113576 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113576 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113576/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113576/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113576 Building REAL300020113577 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113577' /scratch/stefan/7770410/working/building/REAL300020113577 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113577 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113577/0 /scratch/stefan/7770410/working/building/REAL300020113577 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 763) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/763 `/scratch/stefan/7770410/working/3D/763' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=C(CCCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1) `REAL300020113577.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113577 none CC1=CN=C(CCCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 77, 33, 22, 17, 3, 3, 3, 1, 1, 1, 1, 1, 7, 7, 7, 18, 27, 27, 27, 27, 27, 7, 7, 1, 77, 77, 77, 77, 77, 31, 31, 28, 28, 17, 17, 3, 1, 1, 1, 1, 7, 18, 18, 27, 27, 1, 1] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 349 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113577 none CC1=CN=C(CCCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 146, 146, 90, 72, 52, 13, 13, 13, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 146, 146, 146, 146, 146, 85, 86, 83, 83, 52, 52, 13, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 580 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113577 none CC1=CN=C(CCCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 16, 32, 54, 54, 54, 77, 77, 77, 146, 146, 146, 187, 201, 201, 201, 201, 201, 146, 146, 77, 1, 2, 2, 2, 1, 8, 8, 16, 16, 32, 32, 54, 77, 77, 77, 77, 146, 187, 187, 201, 201, 77, 77] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 735 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113577 none CC1=CN=C(CCCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 143, 106, 97, 32, 32, 32, 28, 28, 28, 8, 8, 8, 5, 3, 1, 1, 1, 1, 1, 1, 8, 8, 28, 201, 201, 201, 201, 201, 132, 133, 130, 130, 97, 97, 32, 28, 28, 28, 28, 8, 5, 5, 3, 3, 28, 28] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 821 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113577 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113577/1 /scratch/stefan/7770410/working/building/REAL300020113577 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 764) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/764 `/scratch/stefan/7770410/working/3D/764' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=C(CCCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1) `REAL300020113577.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113577 none CC1=CN=C(CCCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 76, 32, 21, 17, 3, 3, 3, 1, 1, 1, 1, 1, 7, 7, 7, 18, 27, 27, 27, 27, 27, 7, 7, 1, 76, 76, 76, 76, 76, 30, 30, 27, 27, 17, 17, 3, 1, 1, 1, 1, 7, 18, 18, 27, 27, 1, 1] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 344 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113577 none CC1=CN=C(CCCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [145, 145, 145, 145, 90, 72, 53, 13, 13, 13, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 145, 145, 145, 145, 145, 85, 86, 83, 83, 53, 53, 13, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 580 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113577 none CC1=CN=C(CCCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 16, 32, 54, 54, 54, 76, 76, 76, 145, 145, 145, 187, 201, 201, 201, 201, 201, 145, 145, 76, 1, 2, 2, 2, 1, 8, 8, 16, 16, 32, 32, 54, 76, 76, 76, 76, 145, 187, 187, 201, 201, 76, 76] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 732 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113577 none CC1=CN=C(CCCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 143, 106, 97, 33, 33, 33, 29, 29, 29, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 29, 201, 201, 201, 201, 201, 132, 133, 130, 130, 97, 97, 33, 29, 29, 29, 29, 9, 5, 5, 3, 3, 29, 29] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 820 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113577 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113577 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113577/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113577/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113577 Building REAL300020113578 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113578' /scratch/stefan/7770410/working/building/REAL300020113578 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113578 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113578/0 /scratch/stefan/7770410/working/building/REAL300020113578 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 765) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/765 `/scratch/stefan/7770410/working/3D/765' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CN=C2N1) `REAL300020113578.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113578 none CC1=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CN=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 42, 58, 69, 69, 69, 69, 11, 11, 1, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 11, 42, 42, 58, 58, 1, 1, 15, 15] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46]) total number of confs: 279 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113578 none CC1=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CN=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 84, 84, 38, 38, 38, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 11, 84, 84, 84, 84, 84, 84, 84, 84, 38, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 84, 84] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 209 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113578 none CC1=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CN=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 84, 84, 84, 158, 201, 201, 201, 201, 201, 84, 84, 15, 1, 1, 1, 1, 2, 2, 2, 1, 5, 15, 15, 15, 15, 84, 158, 158, 201, 201, 15, 15, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 45, 46, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 761 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113578 none CC1=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CN=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 118, 118, 118, 68, 68, 68, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 68, 201, 201, 201, 201, 201, 201, 201, 201, 118, 68, 68, 68, 68, 13, 6, 6, 4, 4, 68, 68, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 472 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113578 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113578/1 /scratch/stefan/7770410/working/building/REAL300020113578 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 766) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/766 `/scratch/stefan/7770410/working/3D/766' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CN=C2N1) `REAL300020113578.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113578/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113578 none CC1=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CN=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 42, 58, 68, 68, 68, 68, 11, 11, 1, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 11, 42, 42, 58, 58, 1, 1, 15, 15] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46]) total number of confs: 277 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113578 none CC1=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CN=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 84, 84, 38, 38, 38, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 11, 84, 84, 84, 84, 84, 84, 84, 84, 38, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 84, 84] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 211 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113578 none CC1=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CN=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 84, 84, 84, 159, 201, 201, 201, 201, 201, 84, 84, 15, 1, 1, 1, 1, 2, 2, 2, 1, 5, 15, 15, 15, 15, 84, 159, 159, 201, 201, 15, 15, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 45, 46, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 761 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113578 none CC1=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CN=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 119, 119, 119, 68, 68, 68, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 68, 201, 201, 201, 201, 201, 201, 201, 201, 119, 68, 68, 68, 68, 13, 6, 6, 4, 4, 68, 68, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 474 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113578 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113578 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113578/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113578/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113578 Building REAL300020113579 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113579' /scratch/stefan/7770410/working/building/REAL300020113579 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113579 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113579/0 /scratch/stefan/7770410/working/building/REAL300020113579 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/767 `/scratch/stefan/7770410/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CCCC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1) `REAL300020113579.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113579 none COC1CCCC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 73, 73, 73, 73, 73, 40, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 25, 33, 41, 41, 41, 41, 6, 6, 1, 73, 86, 86, 86, 73, 73, 73, 73, 73, 73, 73, 73, 40, 40, 6, 1, 1, 1, 1, 6, 25, 25, 33, 33, 1, 1, 73, 73] 201 rigid atoms, others: [43, 44, 42, 11, 12, 13, 14, 45, 51, 52, 26, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50, 53, 54]) total number of confs: 417 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113579 none COC1CCCC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [138, 125, 125, 125, 125, 125, 96, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 8, 10, 15, 15, 15, 15, 1, 1, 6, 125, 138, 138, 138, 125, 125, 125, 125, 125, 125, 125, 125, 96, 96, 20, 6, 6, 6, 6, 1, 8, 8, 10, 10, 6, 6, 125, 125] 201 rigid atoms, others: [13, 46, 15, 16, 17, 14, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 515 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113579 none COC1CCCC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 5, 25, 25, 25, 73, 73, 73, 125, 125, 125, 176, 198, 201, 201, 201, 201, 125, 125, 73, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 25, 73, 73, 73, 73, 125, 176, 176, 198, 198, 73, 73, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 38, 7, 34, 35, 53, 54, 36, 27, 37, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 682 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113579 none COC1CCCC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 192, 89, 89, 89, 51, 51, 51, 20, 20, 20, 6, 4, 1, 1, 1, 1, 1, 1, 20, 20, 51, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 192, 192, 89, 51, 51, 51, 51, 20, 6, 6, 4, 4, 51, 51, 201, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 713 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113579 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113579/1 /scratch/stefan/7770410/working/building/REAL300020113579 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 768) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/768 `/scratch/stefan/7770410/working/3D/768' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CCCC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1) `REAL300020113579.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113579/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113579 none COC1CCCC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 73, 73, 73, 73, 73, 40, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 25, 33, 42, 42, 42, 42, 6, 6, 1, 73, 86, 86, 86, 73, 73, 73, 73, 73, 73, 73, 73, 40, 40, 6, 1, 1, 1, 1, 6, 25, 25, 33, 33, 1, 1, 73, 73] 201 rigid atoms, others: [43, 44, 42, 11, 12, 13, 14, 45, 51, 52, 26, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50, 53, 54]) total number of confs: 419 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113579 none COC1CCCC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [137, 124, 124, 124, 124, 124, 96, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 8, 10, 15, 15, 15, 15, 1, 1, 6, 124, 137, 137, 137, 124, 124, 124, 124, 124, 124, 124, 124, 96, 96, 20, 6, 6, 6, 6, 1, 8, 8, 10, 10, 6, 6, 124, 124] 201 rigid atoms, others: [13, 46, 15, 16, 17, 14, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 511 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113579 none COC1CCCC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 5, 25, 25, 25, 73, 73, 73, 124, 124, 124, 176, 198, 201, 201, 201, 201, 124, 124, 73, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 25, 73, 73, 73, 73, 124, 176, 176, 198, 198, 73, 73, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 38, 7, 34, 35, 53, 54, 36, 27, 37, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 683 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113579 none COC1CCCC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [196, 196, 196, 196, 196, 196, 187, 86, 86, 86, 49, 49, 49, 21, 21, 21, 6, 4, 1, 1, 1, 1, 1, 1, 21, 21, 49, 196, 196, 196, 196, 196, 196, 196, 196, 196, 196, 196, 196, 187, 187, 86, 49, 49, 49, 49, 21, 6, 6, 4, 4, 49, 49, 196, 196] 196 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 691 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113579 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113579 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113579/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113579/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113579 Building REAL300020113580 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113580' /scratch/stefan/7770410/working/building/REAL300020113580 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113580 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113580/0 /scratch/stefan/7770410/working/building/REAL300020113580 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/769 `/scratch/stefan/7770410/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)C(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113580.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113580 none COCC(C)C(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [150, 130, 86, 76, 87, 28, 76, 28, 28, 9, 9, 9, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 9, 150, 150, 150, 129, 130, 87, 87, 87, 87, 76, 76, 76, 76, 28, 9, 9, 9, 9, 1, 5, 5, 7, 7, 9, 9] 201 rigid atoms, others: [12, 44, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 644 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113580 none COCC(C)C(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 169, 168, 169, 113, 168, 113, 113, 61, 61, 61, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 61, 201, 201, 201, 201, 201, 169, 169, 169, 169, 168, 168, 168, 168, 113, 61, 61, 61, 61, 15, 6, 6, 4, 4, 61, 61] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 788 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113580 none COCC(C)C(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 48, 25, 19, 26, 6, 19, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 23, 35, 35, 35, 35, 35, 9, 9, 1, 73, 73, 73, 47, 48, 26, 26, 26, 26, 19, 19, 19, 19, 6, 1, 1, 1, 1, 9, 23, 23, 35, 35, 1, 1] 201 rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 49, 50, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 407 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113580 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113580/1 /scratch/stefan/7770410/working/building/REAL300020113580 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 770) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/770 `/scratch/stefan/7770410/working/3D/770' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)C(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113580.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113580/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113580 none COCC(C)C(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [149, 130, 86, 76, 87, 28, 76, 28, 28, 9, 9, 9, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 9, 149, 149, 149, 129, 130, 87, 87, 87, 87, 76, 76, 76, 76, 28, 9, 9, 9, 9, 1, 5, 5, 7, 7, 9, 9] 201 rigid atoms, others: [12, 44, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 642 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113580 none COCC(C)C(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 169, 168, 169, 113, 168, 113, 113, 60, 60, 60, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 60, 201, 201, 201, 201, 201, 169, 169, 169, 169, 168, 168, 168, 168, 113, 60, 60, 60, 60, 14, 6, 6, 4, 4, 60, 60] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 789 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113580 none COCC(C)C(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 48, 25, 19, 26, 6, 19, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 23, 35, 35, 35, 35, 35, 9, 9, 1, 72, 72, 72, 47, 48, 26, 26, 26, 26, 19, 19, 19, 19, 6, 1, 1, 1, 1, 9, 23, 23, 35, 35, 1, 1] 201 rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 49, 50, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 405 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113580 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113580 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113580/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113580/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113580 Building REAL300020113581 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113581' /scratch/stefan/7770410/working/building/REAL300020113581 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113581 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113581/0 /scratch/stefan/7770410/working/building/REAL300020113581 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/771 `/scratch/stefan/7770410/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC(F)F)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113581.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113581 none CCC(CC(F)F)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 15, 15, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 87, 33, 87, 106, 116, 116, 33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 95, 95, 95, 95, 95, 87, 106, 106, 116, 33, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 665 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113581 none CCC(CC(F)F)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 15, 15, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [164, 199, 87, 199, 201, 201, 201, 87, 87, 41, 41, 41, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 41, 200, 200, 200, 200, 200, 199, 201, 201, 201, 87, 41, 41, 41, 41, 10, 5, 5, 3, 3, 41, 41] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 998 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113581 none CCC(CC(F)F)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 15, 15, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 20, 6, 20, 28, 36, 36, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 32, 46, 48, 48, 48, 48, 11, 11, 1, 23, 23, 23, 23, 23, 20, 28, 28, 36, 6, 1, 1, 1, 1, 11, 32, 32, 46, 46, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 398 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113581 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113581/1 /scratch/stefan/7770410/working/building/REAL300020113581 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 772) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/772 `/scratch/stefan/7770410/working/3D/772' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC(F)F)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113581.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113581/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113581 none CCC(CC(F)F)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 15, 15, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 87, 33, 87, 106, 116, 116, 33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 94, 94, 94, 94, 94, 87, 106, 106, 116, 33, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 659 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113581 none CCC(CC(F)F)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 15, 15, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 199, 86, 199, 201, 201, 201, 86, 86, 41, 41, 41, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 41, 200, 200, 200, 200, 200, 199, 201, 201, 201, 86, 41, 41, 41, 41, 10, 6, 6, 4, 4, 41, 41] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 1007 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113581 none CCC(CC(F)F)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 15, 15, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 20, 6, 20, 28, 36, 36, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 32, 46, 48, 48, 48, 48, 11, 11, 1, 23, 23, 23, 23, 23, 20, 28, 28, 36, 6, 1, 1, 1, 1, 11, 32, 32, 46, 46, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 398 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113581 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113581 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113581/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113581/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113581 Building REAL300020113582 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113582' /scratch/stefan/7770410/working/building/REAL300020113582 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113582 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113582/0 /scratch/stefan/7770410/working/building/REAL300020113582 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/773 `/scratch/stefan/7770410/working/3D/773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CC(F)F)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113582.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113582 none CC(C)(CC(F)F)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 15, 15, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 26, 60, 60, 101, 106, 106, 26, 26, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 8, 8, 8, 8, 1, 1, 8, 60, 60, 60, 60, 60, 60, 101, 101, 106, 26, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 480 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113582 none CC(C)(CC(F)F)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 15, 15, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [143, 76, 143, 143, 201, 201, 201, 76, 76, 47, 47, 47, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 47, 143, 143, 143, 143, 143, 143, 201, 201, 201, 76, 47, 47, 47, 47, 11, 6, 6, 4, 4, 47, 47] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 861 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113582 none CC(C)(CC(F)F)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 15, 15, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 15, 27, 29, 29, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 22, 35, 36, 36, 36, 36, 8, 8, 1, 15, 15, 15, 15, 15, 15, 27, 27, 29, 6, 1, 1, 1, 1, 8, 22, 22, 35, 35, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 272 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113582 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113582/1 /scratch/stefan/7770410/working/building/REAL300020113582 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 774) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/774 `/scratch/stefan/7770410/working/3D/774' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CC(F)F)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113582.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113582/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113582 none CC(C)(CC(F)F)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 15, 15, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 26, 60, 60, 101, 106, 106, 26, 26, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 8, 8, 8, 8, 1, 1, 8, 60, 60, 60, 60, 60, 60, 101, 101, 106, 26, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 480 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113582 none CC(C)(CC(F)F)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 15, 15, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [144, 76, 144, 144, 201, 201, 201, 76, 76, 48, 48, 48, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 48, 144, 144, 144, 144, 144, 144, 201, 201, 201, 76, 48, 48, 48, 48, 11, 6, 6, 4, 4, 48, 48] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 862 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113582 none CC(C)(CC(F)F)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 15, 15, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 15, 27, 29, 29, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 22, 35, 36, 36, 36, 36, 8, 8, 1, 15, 15, 15, 15, 15, 15, 27, 27, 29, 6, 1, 1, 1, 1, 8, 22, 22, 35, 35, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 272 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113582 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113582 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113582/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113582/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113582 Building REAL300020113583 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113583' /scratch/stefan/7770410/working/building/REAL300020113583 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113583 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113583/0 /scratch/stefan/7770410/working/building/REAL300020113583 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/775 `/scratch/stefan/7770410/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C2CC2)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113583.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113583 none CN1N=CC(C2CC2)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 6, 6, 6, 1, 1, 1, 1, 6, 7, 15, 15, 15, 35, 35, 35, 136, 136, 136, 171, 201, 201, 201, 201, 201, 136, 136, 35, 7, 7, 7, 7, 1, 1, 1, 1, 1, 15, 35, 35, 35, 35, 136, 171, 171, 201, 201, 35, 35] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 36] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 595 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113583 none CN1N=CC(C2CC2)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [176, 176, 176, 176, 176, 176, 201, 201, 106, 106, 106, 40, 40, 40, 10, 10, 10, 6, 3, 1, 1, 1, 1, 1, 1, 10, 10, 40, 176, 176, 176, 176, 201, 201, 201, 201, 201, 106, 40, 40, 40, 40, 10, 6, 6, 3, 3, 40, 40] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 523 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113583 none CN1N=CC(C2CC2)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 21, 21, 35, 35, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 28, 41, 41, 41, 41, 41, 13, 13, 1, 21, 21, 21, 21, 35, 35, 35, 35, 35, 6, 1, 1, 1, 1, 13, 28, 28, 41, 41, 1, 1] 201 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 246 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113583 none CN1N=CC(C2CC2)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 1, 1, 8, 8, 8, 21, 21, 21, 112, 112, 112, 147, 177, 177, 177, 177, 177, 112, 112, 21, 2, 2, 2, 1, 6, 7, 7, 7, 7, 8, 21, 21, 21, 21, 112, 147, 147, 177, 177, 21, 21] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 31] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 558 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113583 none CN1N=CC(C2CC2)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 112, 112, 112, 136, 136, 55, 55, 55, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 112, 112, 112, 112, 136, 136, 136, 136, 136, 55, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 364 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113583 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113583/1 /scratch/stefan/7770410/working/building/REAL300020113583 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 776) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/776 `/scratch/stefan/7770410/working/3D/776' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C2CC2)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113583.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113583/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113583 none CN1N=CC(C2CC2)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 6, 6, 6, 1, 1, 1, 1, 6, 7, 15, 15, 15, 35, 35, 35, 136, 136, 136, 171, 201, 201, 201, 201, 201, 136, 136, 35, 7, 7, 7, 7, 1, 1, 1, 1, 1, 15, 35, 35, 35, 35, 136, 171, 171, 201, 201, 35, 35] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 36] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 592 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113583 none CN1N=CC(C2CC2)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [176, 176, 176, 176, 176, 176, 201, 201, 107, 107, 107, 41, 41, 41, 10, 10, 10, 5, 2, 1, 1, 1, 1, 1, 1, 10, 10, 41, 176, 176, 176, 176, 201, 201, 201, 201, 201, 107, 41, 41, 41, 41, 10, 5, 5, 2, 2, 41, 41] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 522 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113583 none CN1N=CC(C2CC2)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 21, 21, 35, 35, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 28, 40, 40, 40, 40, 40, 13, 13, 1, 21, 21, 21, 21, 35, 35, 35, 35, 35, 6, 1, 1, 1, 1, 13, 28, 28, 40, 40, 1, 1] 201 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 240 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113583 none CN1N=CC(C2CC2)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 1, 1, 8, 8, 8, 21, 21, 21, 112, 112, 112, 147, 177, 177, 177, 177, 177, 112, 112, 21, 2, 2, 2, 1, 6, 7, 7, 7, 7, 8, 21, 21, 21, 21, 112, 147, 147, 177, 177, 21, 21] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 31] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 555 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113583 none CN1N=CC(C2CC2)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 112, 112, 112, 136, 136, 55, 55, 55, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 112, 112, 112, 112, 136, 136, 136, 136, 136, 55, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 364 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113583 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113583 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113583/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113583/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113583 Building REAL300020113584 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113584' /scratch/stefan/7770410/working/building/REAL300020113584 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113584 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113584/0 /scratch/stefan/7770410/working/building/REAL300020113584 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/777 `/scratch/stefan/7770410/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C(F)(F)F)C=NN1) `REAL300020113584.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113584 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C(F)(F)F)C=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 15, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 6, 13, 22, 22, 22, 22, 22, 22, 22, 22, 13, 6, 6, 6, 6, 1, 4, 4, 4, 4, 6, 6, 22, 22] 23 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 62 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113584 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C(F)(F)F)C=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 15, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 7, 7, 7, 5, 5, 5, 4, 2, 1, 1, 1, 1, 1, 1, 5, 5, 7, 14, 23, 23, 23, 23, 23, 23, 23, 23, 14, 7, 7, 7, 7, 5, 4, 4, 2, 2, 7, 7, 23, 23] 23 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 64 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113584 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C(F)(F)F)C=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 15, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 7, 7, 7, 7, 7, 7, 6, 6, 1, 6, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 6, 7, 7, 7, 7, 1, 1, 20, 20] 23 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113584 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C(F)(F)F)C=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 15, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 10, 20, 20, 20, 22, 22, 22, 23, 23, 23, 23, 23, 23, 22, 22, 20, 1, 1, 1, 2, 2, 2, 1, 1, 1, 10, 20, 20, 20, 20, 22, 23, 23, 23, 23, 20, 20, 1, 1] 23 rigid atoms, others: [1, 40, 41, 19, 20, 21, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 71 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113584 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113584/1 /scratch/stefan/7770410/working/building/REAL300020113584 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 778) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/778 `/scratch/stefan/7770410/working/3D/778' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C(F)(F)F)C=NN1) `REAL300020113584.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113584 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C(F)(F)F)C=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 15, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 6, 13, 22, 22, 22, 22, 22, 22, 22, 22, 13, 6, 6, 6, 6, 1, 4, 4, 4, 4, 6, 6, 22, 22] 23 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 62 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113584 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C(F)(F)F)C=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 15, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 7, 7, 7, 5, 5, 5, 4, 2, 1, 1, 1, 1, 1, 1, 5, 5, 7, 14, 23, 23, 23, 23, 23, 23, 23, 23, 14, 7, 7, 7, 7, 5, 4, 4, 2, 2, 7, 7, 23, 23] 23 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 64 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113584 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C(F)(F)F)C=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 15, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 7, 7, 7, 7, 7, 7, 6, 6, 1, 6, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 6, 7, 7, 7, 7, 1, 1, 20, 20] 23 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113584 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C(F)(F)F)C=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 15, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 10, 20, 20, 20, 22, 22, 22, 23, 23, 23, 23, 23, 23, 22, 22, 20, 1, 1, 1, 2, 2, 2, 1, 1, 1, 10, 20, 20, 20, 20, 22, 23, 23, 23, 23, 20, 20, 1, 1] 23 rigid atoms, others: [1, 40, 41, 19, 20, 21, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 71 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113584 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113584 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113584/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113584/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113584 Building REAL300020113585 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113585' /scratch/stefan/7770410/working/building/REAL300020113585 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113585 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113585/0 /scratch/stefan/7770410/working/building/REAL300020113585 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/779 `/scratch/stefan/7770410/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=C(CCCC2)O1) `REAL300020113585.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113585 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=C(CCCC2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 12, 51, 91, 91, 91, 91, 91, 91, 91, 91, 51, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 91, 91, 91, 91, 91, 91, 91, 91, 91] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 241 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113585 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=C(CCCC2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [172, 172, 100, 100, 100, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 100, 172, 201, 201, 201, 201, 201, 201, 201, 201, 172, 100, 100, 100, 100, 18, 6, 6, 4, 4, 100, 100, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 528 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113585 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=C(CCCC2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 63, 82, 100, 100, 100, 100, 12, 12, 1, 6, 14, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 12, 63, 63, 82, 82, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 373 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113585 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=C(CCCC2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 14, 14, 14, 91, 91, 91, 161, 201, 201, 201, 201, 201, 91, 91, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 14, 14, 14, 14, 91, 161, 161, 201, 201, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 711 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113585 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113585/1 /scratch/stefan/7770410/working/building/REAL300020113585 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 780) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/780 `/scratch/stefan/7770410/working/3D/780' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=C(CCCC2)O1) `REAL300020113585.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113585 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=C(CCCC2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 13, 52, 92, 92, 92, 92, 92, 92, 92, 92, 52, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13, 92, 92, 92, 92, 92, 92, 92, 92, 92] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 243 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113585 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=C(CCCC2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 101, 101, 101, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 101, 173, 201, 201, 201, 201, 201, 201, 201, 201, 173, 101, 101, 101, 101, 18, 6, 6, 4, 4, 101, 101, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 528 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113585 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=C(CCCC2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 64, 83, 101, 101, 101, 101, 13, 13, 1, 6, 14, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 13, 64, 64, 83, 83, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 374 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113585 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=C(CCCC2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 14, 14, 14, 92, 92, 92, 162, 201, 201, 201, 201, 201, 92, 92, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 14, 14, 14, 14, 92, 162, 162, 201, 201, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 706 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113585 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113585 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113585/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113585/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113585 Building REAL300020113586 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113586' /scratch/stefan/7770410/working/building/REAL300020113586 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113586 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113586/0 /scratch/stefan/7770410/working/building/REAL300020113586 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/781 `/scratch/stefan/7770410/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CON=C1C1CCCC1) `REAL300020113586.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113586 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CON=C1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 8, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 31, 75, 75, 75, 75, 75, 124, 124, 124, 124, 31, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 75, 124, 124, 124, 124, 124, 124, 124, 124, 124] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 352 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113586 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CON=C1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 8, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 5, 20, 20, 48, 48, 48, 124, 124, 124, 169, 201, 201, 201, 201, 201, 124, 124, 48, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 20, 48, 48, 48, 48, 124, 169, 169, 201, 201, 48, 48, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 687 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113586 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CON=C1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 8, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 46, 46, 46, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 46, 94, 173, 173, 173, 173, 173, 201, 201, 201, 201, 94, 46, 46, 46, 46, 10, 6, 6, 4, 4, 46, 46, 173, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 504 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113586 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CON=C1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 8, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 30, 44, 46, 46, 46, 46, 11, 11, 1, 6, 19, 19, 19, 19, 19, 48, 48, 48, 48, 6, 1, 1, 1, 1, 11, 30, 30, 44, 44, 1, 1, 19, 48, 48, 48, 48, 48, 48, 48, 48, 48] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 293 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113586 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CON=C1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 8, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 19, 19, 19, 75, 75, 75, 128, 168, 170, 170, 170, 170, 75, 75, 19, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 19, 19, 19, 19, 75, 128, 128, 168, 168, 19, 19, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5] 201 rigid atoms, others: [1, 41, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 638 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113586 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113586/1 /scratch/stefan/7770410/working/building/REAL300020113586 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 782) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/782 `/scratch/stefan/7770410/working/3D/782' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CON=C1C1CCCC1) `REAL300020113586.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113586/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113586 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CON=C1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 8, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 31, 76, 76, 76, 76, 76, 125, 125, 125, 125, 31, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 76, 125, 125, 125, 125, 125, 125, 125, 125, 125] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 353 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113586 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CON=C1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 8, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 5, 20, 20, 48, 48, 48, 125, 125, 125, 169, 201, 201, 201, 201, 201, 125, 125, 48, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 20, 48, 48, 48, 48, 125, 169, 169, 201, 201, 48, 48, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 682 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113586 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CON=C1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 8, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 48, 48, 48, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 48, 97, 172, 172, 172, 172, 172, 201, 201, 201, 201, 97, 48, 48, 48, 48, 11, 6, 6, 4, 4, 48, 48, 172, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 509 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113586 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CON=C1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 8, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 30, 44, 46, 46, 46, 46, 11, 11, 1, 6, 19, 19, 19, 19, 19, 48, 48, 48, 48, 6, 1, 1, 1, 1, 11, 30, 30, 44, 44, 1, 1, 19, 48, 48, 48, 48, 48, 48, 48, 48, 48] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 293 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113586 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CON=C1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 8, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 19, 19, 19, 76, 76, 76, 129, 168, 170, 170, 170, 170, 76, 76, 19, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 19, 19, 19, 19, 76, 129, 129, 168, 168, 19, 19, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5] 201 rigid atoms, others: [1, 41, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 633 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113586 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113586 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113586/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113586/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113586 Building REAL300020113587 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113587' /scratch/stefan/7770410/working/building/REAL300020113587 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113587 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113587/0 /scratch/stefan/7770410/working/building/REAL300020113587 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/783 `/scratch/stefan/7770410/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(=O)NC(C2CC2)=C1) `REAL300020113587.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113587 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(=O)NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 9, 22, 65, 65, 65, 65, 65, 65, 87, 87, 65, 22, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 65, 65, 87, 87, 87, 87, 87, 65] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 238 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113587 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(=O)NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 3, 9, 9, 20, 20, 20, 87, 87, 87, 150, 201, 201, 201, 201, 201, 87, 87, 20, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 9, 20, 20, 20, 20, 87, 150, 150, 201, 201, 20, 20, 3, 3, 1, 1, 1, 1, 1, 3] 201 rigid atoms, others: [43, 44, 45, 46, 47, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48]) total number of confs: 788 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113587 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(=O)NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 40, 40, 40, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 40, 69, 194, 194, 194, 194, 194, 194, 201, 201, 194, 69, 40, 40, 40, 40, 9, 4, 4, 2, 2, 40, 40, 194, 194, 201, 201, 201, 201, 201, 194] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 404 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113587 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(=O)NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 27, 40, 40, 40, 40, 40, 9, 9, 1, 5, 12, 12, 12, 12, 12, 12, 20, 20, 12, 5, 1, 1, 1, 1, 9, 27, 27, 40, 40, 1, 1, 12, 12, 20, 20, 20, 20, 20, 12] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113587 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(=O)NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 12, 12, 12, 65, 65, 65, 135, 194, 194, 194, 194, 194, 65, 65, 12, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 5, 12, 12, 12, 12, 65, 135, 135, 194, 194, 12, 12, 1, 1, 3, 3, 3, 3, 3, 1] 201 rigid atoms, others: [1, 41, 42, 48, 19, 20, 21, 22, 23, 24, 25, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47]) total number of confs: 798 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113587 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113587/1 /scratch/stefan/7770410/working/building/REAL300020113587 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 784) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/784 `/scratch/stefan/7770410/working/3D/784' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(=O)NC(C2CC2)=C1) `REAL300020113587.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113587 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(=O)NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 9, 22, 65, 65, 65, 65, 65, 65, 87, 87, 65, 22, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 65, 65, 87, 87, 87, 87, 87, 65] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 238 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113587 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(=O)NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 3, 9, 9, 20, 20, 20, 87, 87, 87, 150, 201, 201, 201, 201, 201, 87, 87, 20, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 9, 20, 20, 20, 20, 87, 150, 150, 201, 201, 20, 20, 3, 3, 1, 1, 1, 1, 1, 3] 201 rigid atoms, others: [43, 44, 45, 46, 47, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48]) total number of confs: 788 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113587 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(=O)NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 40, 40, 40, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 40, 69, 194, 194, 194, 194, 194, 194, 201, 201, 194, 69, 40, 40, 40, 40, 9, 4, 4, 2, 2, 40, 40, 194, 194, 201, 201, 201, 201, 201, 194] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 404 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113587 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(=O)NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 27, 40, 40, 40, 40, 40, 9, 9, 1, 5, 12, 12, 12, 12, 12, 12, 20, 20, 12, 5, 1, 1, 1, 1, 9, 27, 27, 40, 40, 1, 1, 12, 12, 20, 20, 20, 20, 20, 12] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113587 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(=O)NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 12, 12, 12, 65, 65, 65, 135, 194, 194, 194, 194, 194, 65, 65, 12, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 5, 12, 12, 12, 12, 65, 135, 135, 194, 194, 12, 12, 1, 1, 3, 3, 3, 3, 3, 1] 201 rigid atoms, others: [1, 41, 42, 48, 19, 20, 21, 22, 23, 24, 25, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47]) total number of confs: 798 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113587 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113587 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113587/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113587/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113587 Building REAL300020113588 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113588' /scratch/stefan/7770410/working/building/REAL300020113588 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113588 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113588/0 /scratch/stefan/7770410/working/building/REAL300020113588 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 785) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/785 `/scratch/stefan/7770410/working/3D/785' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2=NC=NC=C2C1) `REAL300020113588.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113588 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2=NC=NC=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 8, 1, 8, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 33, 101, 101, 101, 101, 101, 101, 101, 101, 101, 33, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 101, 101, 101, 101, 101, 101, 101, 101, 101] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 301 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113588 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2=NC=NC=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 8, 1, 8, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 52, 52, 52, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 52, 108, 201, 201, 201, 201, 201, 201, 201, 201, 201, 108, 52, 52, 52, 52, 10, 6, 6, 4, 4, 52, 52, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 607 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113588 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2=NC=NC=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 8, 1, 8, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 47, 52, 52, 52, 52, 11, 11, 1, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 31, 31, 47, 47, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113588 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2=NC=NC=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 8, 1, 8, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 22, 22, 22, 101, 101, 101, 159, 201, 201, 201, 201, 201, 101, 101, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 22, 22, 22, 22, 101, 159, 159, 201, 201, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 719 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113588 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113588/1 /scratch/stefan/7770410/working/building/REAL300020113588 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 786) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/786 `/scratch/stefan/7770410/working/3D/786' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2=NC=NC=C2C1) `REAL300020113588.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113588/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113588 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2=NC=NC=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 8, 1, 8, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 33, 101, 101, 101, 101, 101, 101, 101, 101, 101, 33, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 101, 101, 101, 101, 101, 101, 101, 101, 101] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 303 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113588 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2=NC=NC=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 8, 1, 8, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 53, 53, 53, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 53, 110, 201, 201, 201, 201, 201, 201, 201, 201, 201, 110, 53, 53, 53, 53, 11, 6, 6, 4, 4, 53, 53, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 605 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113588 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2=NC=NC=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 8, 1, 8, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 47, 52, 52, 52, 52, 11, 11, 1, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 31, 31, 47, 47, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113588 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2=NC=NC=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 8, 1, 8, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 22, 22, 22, 101, 101, 101, 159, 201, 201, 201, 201, 201, 101, 101, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 22, 22, 22, 22, 101, 159, 159, 201, 201, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 719 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113588 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113588 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113588/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113588/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113588 Building REAL300020113589 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113589' /scratch/stefan/7770410/working/building/REAL300020113589 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113589 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113589/0 /scratch/stefan/7770410/working/building/REAL300020113589 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/787 `/scratch/stefan/7770410/working/3D/787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1COCC2) `REAL300020113589.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113589 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1COCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 58, 125, 125, 88, 125, 125, 125, 125, 125, 125, 58, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 125, 125, 125, 125, 125, 125, 125, 125, 125] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 441 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113589 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1COCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [143, 143, 58, 58, 58, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 58, 143, 201, 201, 171, 201, 201, 201, 201, 201, 201, 143, 58, 58, 58, 58, 12, 6, 6, 4, 4, 58, 58, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 606 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113589 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1COCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 35, 52, 56, 56, 56, 56, 13, 13, 1, 6, 24, 24, 12, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 13, 35, 35, 52, 52, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 303 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113589 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1COCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 24, 24, 24, 125, 125, 125, 169, 201, 201, 201, 201, 201, 125, 125, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 24, 24, 24, 24, 125, 169, 169, 201, 201, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 602 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113589 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113589/1 /scratch/stefan/7770410/working/building/REAL300020113589 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 788) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/788 `/scratch/stefan/7770410/working/3D/788' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1COCC2) `REAL300020113589.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113589/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113589 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1COCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 58, 124, 124, 88, 124, 124, 124, 124, 124, 124, 58, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 124, 124, 124, 124, 124, 124, 124, 124, 124] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 437 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113589 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1COCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [142, 142, 56, 56, 56, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 56, 142, 201, 201, 171, 201, 201, 201, 201, 201, 201, 142, 56, 56, 56, 56, 11, 6, 6, 4, 4, 56, 56, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 609 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113589 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1COCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 34, 51, 55, 55, 55, 55, 13, 13, 1, 6, 25, 25, 12, 25, 25, 25, 25, 25, 25, 6, 1, 1, 1, 1, 13, 34, 34, 51, 51, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 303 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113589 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1COCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 25, 25, 25, 124, 124, 124, 169, 201, 201, 201, 201, 201, 124, 124, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 25, 25, 25, 25, 124, 169, 169, 201, 201, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 605 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113589 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113589 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113589/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113589/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113589 Building REAL300020113590 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113590' /scratch/stefan/7770410/working/building/REAL300020113590 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113590 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113590/0 /scratch/stefan/7770410/working/building/REAL300020113590 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 789) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/789 `/scratch/stefan/7770410/working/3D/789' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCC1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113590.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113590 none CC1CCCC1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 70, 70, 42, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 19, 26, 26, 26, 26, 26, 13, 13, 1, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 42, 42, 6, 1, 1, 1, 1, 13, 19, 19, 26, 26, 1, 1] 201 rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 49, 50, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 327 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113590 none CC1CCCC1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [179, 179, 179, 179, 179, 169, 48, 48, 48, 13, 13, 13, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 1, 1, 13, 179, 179, 179, 179, 179, 179, 179, 179, 179, 179, 179, 169, 169, 48, 13, 13, 13, 13, 1, 3, 3, 5, 5, 13, 13] 201 rigid atoms, others: [12, 44, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 662 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113590 none CC1CCCC1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 25, 25, 25, 70, 70, 70, 179, 179, 179, 188, 201, 201, 201, 201, 201, 179, 179, 70, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 25, 70, 70, 70, 70, 179, 188, 188, 201, 201, 70, 70] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 35, 36, 33, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 483 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113590 none CC1CCCC1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 192, 63, 63, 63, 26, 26, 26, 5, 5, 5, 4, 2, 1, 1, 1, 1, 1, 1, 5, 5, 26, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 192, 192, 63, 26, 26, 26, 26, 5, 4, 4, 2, 2, 26, 26] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 748 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113590 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113590/1 /scratch/stefan/7770410/working/building/REAL300020113590 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 790) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/790 `/scratch/stefan/7770410/working/3D/790' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCC1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113590.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113590 none CC1CCCC1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 71, 42, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 19, 26, 26, 26, 26, 26, 13, 13, 1, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 42, 42, 6, 1, 1, 1, 1, 13, 19, 19, 26, 26, 1, 1] 201 rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 49, 50, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 329 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113590 none CC1CCCC1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [179, 179, 179, 179, 179, 168, 48, 48, 48, 13, 13, 13, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 1, 1, 13, 179, 179, 179, 179, 179, 179, 179, 179, 179, 179, 179, 168, 168, 48, 13, 13, 13, 13, 1, 3, 3, 5, 5, 13, 13] 201 rigid atoms, others: [12, 44, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 663 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113590 none CC1CCCC1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 26, 26, 26, 71, 71, 71, 179, 179, 179, 188, 201, 201, 201, 201, 201, 179, 179, 71, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 71, 71, 71, 71, 179, 188, 188, 201, 201, 71, 71] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 35, 36, 33, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 486 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113590 none CC1CCCC1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 191, 63, 63, 63, 26, 26, 26, 5, 5, 5, 4, 2, 1, 1, 1, 1, 1, 1, 5, 5, 26, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 191, 191, 63, 26, 26, 26, 26, 5, 4, 4, 2, 2, 26, 26] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 749 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113590 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113590 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113590/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113590/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113590 Building REAL300020113591 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113591' /scratch/stefan/7770410/working/building/REAL300020113591 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113591 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113591/0 /scratch/stefan/7770410/working/building/REAL300020113591 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 791) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/791 `/scratch/stefan/7770410/working/3D/791' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(F)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113591.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113591 none COC1=CC=CC(F)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 31, 31, 31, 10, 31, 31, 31, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 32, 45, 46, 46, 46, 46, 11, 11, 1, 38, 38, 38, 31, 31, 31, 6, 1, 1, 1, 1, 11, 32, 32, 45, 45, 1, 1] 201 rigid atoms, others: [45, 35, 36, 37, 38, 44, 11, 12, 13, 14, 15, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 286 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113591 none COC1=CC=CC(F)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 101, 101, 101, 53, 101, 101, 101, 30, 30, 30, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 115, 115, 115, 101, 101, 101, 30, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [39, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 384 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113591 none COC1=CC=CC(F)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 31, 31, 31, 101, 101, 101, 170, 201, 201, 201, 201, 201, 101, 101, 31, 4, 4, 4, 1, 1, 1, 12, 31, 31, 31, 31, 101, 170, 170, 201, 201, 31, 31] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 8, 9, 7, 31] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 735 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113591 none COC1=CC=CC(F)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 154, 201, 201, 201, 86, 86, 86, 47, 47, 47, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 47, 201, 201, 201, 201, 201, 201, 86, 47, 47, 47, 47, 10, 5, 5, 3, 3, 47, 47] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 585 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113591 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113591/1 /scratch/stefan/7770410/working/building/REAL300020113591 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 792) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/792 `/scratch/stefan/7770410/working/3D/792' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(F)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113591.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113591/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113591 none COC1=CC=CC(F)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 31, 31, 31, 10, 31, 31, 31, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 32, 45, 46, 46, 46, 46, 11, 11, 1, 38, 38, 38, 31, 31, 31, 6, 1, 1, 1, 1, 11, 32, 32, 45, 45, 1, 1] 201 rigid atoms, others: [45, 35, 36, 37, 38, 44, 11, 12, 13, 14, 15, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 286 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113591 none COC1=CC=CC(F)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 102, 102, 102, 54, 102, 102, 102, 30, 30, 30, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 116, 116, 116, 102, 102, 102, 30, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [39, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 388 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113591 none COC1=CC=CC(F)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 31, 31, 31, 102, 102, 102, 170, 201, 201, 201, 201, 201, 102, 102, 31, 4, 4, 4, 1, 1, 1, 12, 31, 31, 31, 31, 102, 170, 170, 201, 201, 31, 31] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 8, 9, 7, 31] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 734 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113591 none COC1=CC=CC(F)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 156, 201, 201, 201, 86, 86, 86, 47, 47, 47, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 47, 201, 201, 201, 201, 201, 201, 86, 47, 47, 47, 47, 10, 5, 5, 3, 3, 47, 47] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 581 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113591 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113591 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113591/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113591/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113591 Building REAL300020113592 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113592' /scratch/stefan/7770410/working/building/REAL300020113592 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113592 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113592/0 /scratch/stefan/7770410/working/building/REAL300020113592 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/793 `/scratch/stefan/7770410/working/3D/793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)C1CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113592.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113592 none O=C(CNC(=O)C1CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 20, 22, 22, 22, 46, 46, 46, 46, 1, 1, 1, 1, 1, 7, 7, 7, 20, 32, 32, 32, 32, 32, 7, 7, 1, 20, 20, 22, 46, 46, 46, 46, 46, 46, 46, 46, 46, 5, 1, 1, 1, 1, 7, 20, 20, 32, 32, 1, 1] 201 rigid atoms, others: [43, 41, 42, 11, 12, 13, 14, 15, 50, 51, 27, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 270 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113592 none O=C(CNC(=O)C1CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 71, 71, 71, 71, 112, 112, 112, 112, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 71, 71, 71, 112, 112, 112, 112, 112, 112, 112, 112, 112, 17, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7] 201 rigid atoms, others: [45, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 395 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113592 none O=C(CNC(=O)C1CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 17, 7, 7, 1, 7, 1, 1, 1, 1, 1, 29, 29, 46, 46, 46, 112, 112, 112, 168, 201, 201, 201, 201, 201, 112, 112, 46, 17, 17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 46, 46, 46, 46, 112, 168, 168, 201, 201, 46, 46] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 39, 36, 38, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 759 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113592 none O=C(CNC(=O)C1CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 139, 139, 139, 139, 201, 201, 201, 201, 32, 32, 32, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 32, 139, 139, 139, 201, 201, 201, 201, 201, 201, 201, 201, 201, 50, 32, 32, 32, 32, 9, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 698 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113592 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113592/1 /scratch/stefan/7770410/working/building/REAL300020113592 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 794) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/794 `/scratch/stefan/7770410/working/3D/794' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)C1CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113592.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113592 none O=C(CNC(=O)C1CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 20, 22, 22, 22, 46, 46, 46, 46, 1, 1, 1, 1, 1, 7, 7, 7, 20, 32, 32, 32, 32, 32, 7, 7, 1, 20, 20, 22, 46, 46, 46, 46, 46, 46, 46, 46, 46, 5, 1, 1, 1, 1, 7, 20, 20, 32, 32, 1, 1] 201 rigid atoms, others: [43, 41, 42, 11, 12, 13, 14, 15, 50, 51, 27, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 270 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113592 none O=C(CNC(=O)C1CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 71, 71, 71, 71, 112, 112, 112, 112, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 71, 71, 71, 112, 112, 112, 112, 112, 112, 112, 112, 112, 17, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7] 201 rigid atoms, others: [45, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 395 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113592 none O=C(CNC(=O)C1CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 17, 7, 7, 1, 7, 1, 1, 1, 1, 1, 29, 29, 46, 46, 46, 112, 112, 112, 168, 201, 201, 201, 201, 201, 112, 112, 46, 17, 17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 46, 46, 46, 46, 112, 168, 168, 201, 201, 46, 46] 201 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 39, 36, 38, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 756 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113592 none O=C(CNC(=O)C1CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 139, 139, 139, 139, 201, 201, 201, 201, 31, 31, 31, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 31, 139, 139, 139, 201, 201, 201, 201, 201, 201, 201, 201, 201, 50, 31, 31, 31, 31, 8, 4, 4, 2, 2, 31, 31] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 698 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113592 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113592 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113592/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113592/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113592 Building REAL300020113593 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113593' /scratch/stefan/7770410/working/building/REAL300020113593 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113593 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113593/0 /scratch/stefan/7770410/working/building/REAL300020113593 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/795 `/scratch/stefan/7770410/working/3D/795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CO1) `REAL300020113593.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113593 none CC1=C(C(=O)NCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 28, 28, 28, 24, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 18, 29, 29, 29, 29, 29, 7, 7, 1, 57, 57, 57, 57, 57, 57, 28, 24, 24, 5, 1, 1, 1, 1, 7, 18, 18, 29, 29, 1, 1, 57, 57] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 272 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113593 none CC1=C(C(=O)NCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 76, 76, 76, 73, 17, 17, 17, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 128, 128, 128, 128, 128, 128, 76, 73, 73, 17, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7, 128, 128] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 396 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113593 none CC1=C(C(=O)NCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 14, 35, 34, 34, 57, 57, 57, 128, 128, 128, 176, 201, 201, 201, 201, 201, 128, 128, 57, 1, 1, 1, 2, 2, 2, 4, 14, 14, 35, 57, 57, 57, 57, 128, 176, 176, 201, 201, 57, 57, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 47, 48, 26, 27, 28] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 711 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113593 none CC1=C(C(=O)NCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 127, 127, 127, 127, 50, 50, 50, 32, 32, 32, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 32, 201, 201, 201, 201, 201, 201, 127, 127, 127, 50, 32, 32, 32, 32, 8, 4, 4, 2, 2, 32, 32, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 619 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113593 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113593/1 /scratch/stefan/7770410/working/building/REAL300020113593 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 796) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/796 `/scratch/stefan/7770410/working/3D/796' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CO1) `REAL300020113593.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113593/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113593 none CC1=C(C(=O)NCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 28, 28, 28, 24, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 18, 29, 29, 29, 29, 29, 7, 7, 1, 57, 57, 57, 57, 57, 57, 28, 24, 24, 5, 1, 1, 1, 1, 7, 18, 18, 29, 29, 1, 1, 57, 57] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 272 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113593 none CC1=C(C(=O)NCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [130, 130, 78, 78, 78, 75, 19, 19, 19, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 130, 130, 130, 130, 130, 130, 78, 75, 75, 19, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7, 130, 130] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 400 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113593 none CC1=C(C(=O)NCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 14, 35, 34, 34, 57, 57, 57, 130, 130, 130, 175, 201, 201, 201, 201, 201, 130, 130, 57, 1, 1, 1, 2, 2, 2, 4, 14, 14, 35, 57, 57, 57, 57, 130, 175, 175, 201, 201, 57, 57, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 47, 48, 26, 27, 28] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 702 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113593 none CC1=C(C(=O)NCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 127, 127, 127, 127, 51, 51, 51, 32, 32, 32, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 32, 201, 201, 201, 201, 201, 201, 127, 127, 127, 51, 32, 32, 32, 32, 8, 4, 4, 2, 2, 32, 32, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 615 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113593 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113593 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113593/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113593/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113593 Building REAL300020113594 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113594' /scratch/stefan/7770410/working/building/REAL300020113594 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113594 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113594/0 /scratch/stefan/7770410/working/building/REAL300020113594 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/797 `/scratch/stefan/7770410/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)C1=COC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113594.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113594 none O=C(CNC(=O)C1=COC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 1, 1, 12, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 25, 29, 29, 29, 60, 60, 60, 60, 1, 1, 1, 1, 1, 8, 8, 8, 21, 33, 33, 33, 33, 33, 8, 8, 1, 25, 25, 29, 60, 60, 60, 5, 1, 1, 1, 1, 8, 21, 21, 33, 33, 1, 1] 201 rigid atoms, others: [45, 35, 36, 37, 38, 44, 11, 12, 13, 14, 15, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 287 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113594 none O=C(CNC(=O)C1=COC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 1, 1, 12, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 81, 92, 92, 92, 138, 138, 138, 138, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 81, 81, 92, 138, 138, 138, 19, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [39, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 439 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113594 none O=C(CNC(=O)C1=COC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 1, 1, 12, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 35, 35, 60, 60, 60, 138, 138, 138, 180, 201, 201, 201, 201, 201, 138, 138, 60, 17, 17, 5, 1, 1, 1, 36, 60, 60, 60, 60, 138, 180, 180, 201, 201, 60, 60] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 671 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113594 none O=C(CNC(=O)C1=COC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 1, 1, 12, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 178, 179, 179, 179, 201, 201, 201, 201, 34, 34, 34, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 34, 178, 178, 179, 201, 201, 201, 61, 34, 34, 34, 34, 8, 4, 4, 2, 2, 34, 34] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 688 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113594 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113594/1 /scratch/stefan/7770410/working/building/REAL300020113594 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 798) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/798 `/scratch/stefan/7770410/working/3D/798' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)C1=COC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113594.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113594/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113594 none O=C(CNC(=O)C1=COC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 1, 1, 12, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 25, 29, 29, 29, 61, 61, 61, 61, 1, 1, 1, 1, 1, 8, 8, 8, 21, 33, 33, 33, 33, 33, 8, 8, 1, 25, 25, 29, 61, 61, 61, 5, 1, 1, 1, 1, 8, 21, 21, 33, 33, 1, 1] 201 rigid atoms, others: [45, 35, 36, 37, 38, 44, 11, 12, 13, 14, 15, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 288 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113594 none O=C(CNC(=O)C1=COC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 1, 1, 12, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 81, 92, 92, 92, 139, 139, 139, 139, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 81, 81, 92, 139, 139, 139, 19, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [39, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 441 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113594 none O=C(CNC(=O)C1=COC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 1, 1, 12, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 35, 35, 61, 61, 61, 139, 139, 139, 180, 201, 201, 201, 201, 201, 139, 139, 61, 17, 17, 5, 1, 1, 1, 36, 61, 61, 61, 61, 139, 180, 180, 201, 201, 61, 61] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 669 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113594 none O=C(CNC(=O)C1=COC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 1, 1, 12, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 179, 180, 180, 180, 201, 201, 201, 201, 33, 33, 33, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 33, 179, 179, 180, 201, 201, 201, 60, 33, 33, 33, 33, 7, 4, 4, 2, 2, 33, 33] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 694 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113594 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113594 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113594/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113594/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113594 Building REAL300020113595 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113595' /scratch/stefan/7770410/working/building/REAL300020113595 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113595 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113595/0 /scratch/stefan/7770410/working/building/REAL300020113595 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/799 `/scratch/stefan/7770410/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113595.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113595 none CCC(=O)NC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 57, 57, 57, 55, 21, 55, 21, 21, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 106, 106, 106, 106, 106, 57, 55, 55, 55, 55, 21, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 498 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113595 none CCC(=O)NC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 133, 133, 133, 132, 65, 132, 65, 65, 35, 35, 35, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 35, 201, 201, 201, 201, 201, 133, 132, 132, 132, 132, 65, 35, 35, 35, 35, 8, 4, 4, 2, 2, 35, 35] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 930 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113595 none CCC(=O)NC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 18, 18, 18, 17, 5, 17, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 35, 35, 35, 35, 8, 8, 1, 46, 46, 46, 46, 46, 18, 17, 17, 17, 17, 5, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 323 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113595 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113595/1 /scratch/stefan/7770410/working/building/REAL300020113595 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 800) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/800 `/scratch/stefan/7770410/working/3D/800' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113595.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113595/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113595 none CCC(=O)NC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 57, 57, 57, 55, 21, 55, 21, 21, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 108, 108, 108, 108, 108, 57, 55, 55, 55, 55, 21, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 507 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113595 none CCC(=O)NC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 134, 134, 134, 133, 65, 133, 65, 65, 35, 35, 35, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 35, 201, 201, 201, 201, 201, 134, 133, 133, 133, 133, 65, 35, 35, 35, 35, 9, 4, 4, 2, 2, 35, 35] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 930 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113595 none CCC(=O)NC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 18, 18, 18, 17, 5, 17, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 35, 35, 35, 35, 8, 8, 1, 46, 46, 46, 46, 46, 18, 17, 17, 17, 17, 5, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 323 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113595 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113595 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113595/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113595/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113595 Building REAL300020113596 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113596' /scratch/stefan/7770410/working/building/REAL300020113596 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113596 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113596/0 /scratch/stefan/7770410/working/building/REAL300020113596 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/801 `/scratch/stefan/7770410/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(NC(=O)C1=COC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113596.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113596 none CC(NC(=O)C1=COC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 6, 19, 21, 21, 21, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 25, 39, 39, 39, 39, 39, 8, 8, 1, 19, 19, 19, 19, 21, 50, 50, 50, 6, 1, 1, 1, 1, 8, 25, 25, 39, 39, 1, 1] 201 rigid atoms, others: [48, 38, 39, 40, 41, 12, 13, 14, 15, 16, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 279 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113596 none CC(NC(=O)C1=COC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 25, 70, 75, 75, 75, 127, 127, 127, 127, 25, 25, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 70, 70, 70, 70, 75, 127, 127, 127, 25, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 387 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113596 none CC(NC(=O)C1=COC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 11, 24, 24, 24, 50, 50, 50, 127, 127, 127, 176, 201, 201, 201, 201, 201, 127, 127, 50, 11, 11, 11, 11, 5, 1, 1, 1, 24, 50, 50, 50, 50, 127, 176, 176, 201, 201, 50, 50] 201 rigid atoms, others: [34, 3, 36, 5, 6, 7, 8, 9, 35] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 683 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113596 none CC(NC(=O)C1=COC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [154, 76, 154, 157, 157, 157, 201, 201, 201, 201, 76, 76, 41, 41, 41, 11, 11, 11, 5, 3, 1, 1, 1, 1, 1, 1, 11, 11, 41, 154, 154, 154, 154, 157, 201, 201, 201, 76, 41, 41, 41, 41, 11, 5, 5, 3, 3, 41, 41] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 669 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113596 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113596/1 /scratch/stefan/7770410/working/building/REAL300020113596 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 802) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/802 `/scratch/stefan/7770410/working/3D/802' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(NC(=O)C1=COC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113596.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113596 none CC(NC(=O)C1=COC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 6, 19, 21, 21, 21, 51, 51, 51, 51, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 25, 39, 39, 39, 39, 39, 8, 8, 1, 19, 19, 19, 19, 21, 51, 51, 51, 6, 1, 1, 1, 1, 8, 25, 25, 39, 39, 1, 1] 201 rigid atoms, others: [48, 38, 39, 40, 41, 12, 13, 14, 15, 16, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 281 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113596 none CC(NC(=O)C1=COC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 25, 70, 75, 75, 75, 128, 128, 128, 128, 25, 25, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 70, 70, 70, 70, 75, 128, 128, 128, 25, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 389 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113596 none CC(NC(=O)C1=COC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 11, 25, 25, 25, 51, 51, 51, 128, 128, 128, 176, 201, 201, 201, 201, 201, 128, 128, 51, 11, 11, 11, 11, 5, 1, 1, 1, 25, 51, 51, 51, 51, 128, 176, 176, 201, 201, 51, 51] 201 rigid atoms, others: [34, 3, 36, 5, 6, 7, 8, 9, 35] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 682 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113596 none CC(NC(=O)C1=COC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [155, 74, 155, 158, 158, 158, 201, 201, 201, 201, 74, 74, 39, 39, 39, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 39, 155, 155, 155, 155, 158, 201, 201, 201, 74, 39, 39, 39, 39, 9, 5, 5, 3, 3, 39, 39] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 676 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113596 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113596 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113596/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113596/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113596 Building REAL300020113597 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113597' /scratch/stefan/7770410/working/building/REAL300020113597 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113597 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113597/0 /scratch/stefan/7770410/working/building/REAL300020113597 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/803 `/scratch/stefan/7770410/working/3D/803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113597.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113597 none CC(C)C(=O)N(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 71, 100, 70, 71, 49, 70, 16, 16, 16, 7, 7, 7, 1, 1, 1, 1, 1, 7, 9, 12, 12, 12, 12, 1, 1, 7, 100, 100, 100, 100, 100, 100, 100, 70, 70, 70, 49, 49, 16, 7, 7, 7, 7, 1, 7, 7, 9, 9, 7, 7] 201 rigid atoms, others: [44, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 470 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113597 none CC(C)C(=O)N(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 175, 201, 88, 88, 88, 56, 56, 56, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 56, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 175, 175, 88, 56, 56, 56, 56, 12, 6, 6, 4, 4, 56, 56] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 754 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113597 none CC(C)C(=O)N(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 26, 41, 25, 26, 13, 25, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 34, 46, 55, 55, 55, 55, 7, 7, 1, 41, 41, 41, 41, 41, 41, 41, 25, 25, 25, 13, 13, 5, 1, 1, 1, 1, 7, 34, 34, 46, 46, 1, 1] 201 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 49, 50, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 366 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113597 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113597/1 /scratch/stefan/7770410/working/building/REAL300020113597 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 804) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/804 `/scratch/stefan/7770410/working/3D/804' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113597.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113597 none CC(C)C(=O)N(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 71, 100, 70, 71, 49, 70, 16, 16, 16, 7, 7, 7, 1, 1, 1, 1, 1, 7, 9, 12, 12, 12, 12, 1, 1, 7, 100, 100, 100, 100, 100, 100, 100, 70, 70, 70, 49, 49, 16, 7, 7, 7, 7, 1, 7, 7, 9, 9, 7, 7] 201 rigid atoms, others: [44, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 470 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113597 none CC(C)C(=O)N(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 175, 201, 88, 88, 88, 56, 56, 56, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 56, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 175, 175, 88, 56, 56, 56, 56, 12, 6, 6, 4, 4, 56, 56] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 754 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113597 none CC(C)C(=O)N(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 26, 41, 25, 26, 13, 25, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 34, 46, 55, 55, 55, 55, 7, 7, 1, 41, 41, 41, 41, 41, 41, 41, 25, 25, 25, 13, 13, 5, 1, 1, 1, 1, 7, 34, 34, 46, 46, 1, 1] 201 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 49, 50, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 366 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113597 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113597 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113597/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113597/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113597 Building REAL300020113598 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113598' /scratch/stefan/7770410/working/building/REAL300020113598 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113598 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113598/0 /scratch/stefan/7770410/working/building/REAL300020113598 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/805 `/scratch/stefan/7770410/working/3D/805' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)NCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113598.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113598 none CCS(=O)(=O)NCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 78, 78, 78, 78, 78, 26, 26, 26, 7, 7, 7, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 7, 93, 93, 93, 93, 93, 78, 78, 78, 26, 7, 7, 7, 7, 1, 8, 8, 10, 10, 7, 7] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 413 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113598 none CCS(=O)(=O)NCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 110, 110, 110, 54, 54, 54, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 54, 201, 201, 201, 201, 201, 201, 201, 201, 110, 54, 54, 54, 54, 14, 6, 6, 4, 4, 54, 54] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 741 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113598 none CCS(=O)(=O)NCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 23, 23, 23, 23, 23, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 32, 44, 54, 54, 54, 54, 7, 7, 1, 28, 28, 28, 28, 28, 23, 23, 23, 6, 1, 1, 1, 1, 7, 32, 32, 44, 44, 1, 1] 201 rigid atoms, others: [45, 35, 36, 37, 38, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 298 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113598 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113598/1 /scratch/stefan/7770410/working/building/REAL300020113598 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 806) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/806 `/scratch/stefan/7770410/working/3D/806' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)NCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113598.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113598/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113598 none CCS(=O)(=O)NCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 79, 79, 79, 79, 79, 26, 26, 26, 7, 7, 7, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 7, 94, 94, 94, 94, 94, 79, 79, 79, 26, 7, 7, 7, 7, 1, 8, 8, 10, 10, 7, 7] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 416 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113598 none CCS(=O)(=O)NCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 110, 110, 110, 55, 55, 55, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 55, 201, 201, 201, 201, 201, 201, 201, 201, 110, 55, 55, 55, 55, 13, 6, 6, 4, 4, 55, 55] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 744 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113598 none CCS(=O)(=O)NCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 23, 23, 23, 23, 23, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 32, 44, 55, 55, 55, 55, 7, 7, 1, 28, 28, 28, 28, 28, 23, 23, 23, 6, 1, 1, 1, 1, 7, 32, 32, 44, 44, 1, 1] 201 rigid atoms, others: [45, 35, 36, 37, 38, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113598 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113598 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113598/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113598/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113598 Building REAL300020113599 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113599' /scratch/stefan/7770410/working/building/REAL300020113599 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113599 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113599/0 /scratch/stefan/7770410/working/building/REAL300020113599 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/807 `/scratch/stefan/7770410/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)NCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113599.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113599 none CS(=O)(=O)NCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [148, 127, 148, 148, 55, 49, 12, 12, 12, 7, 7, 7, 1, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 1, 1, 7, 148, 148, 148, 127, 55, 55, 49, 49, 12, 7, 7, 7, 7, 1, 6, 6, 6, 6, 7, 7] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 567 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113599 none CS(=O)(=O)NCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 194, 201, 201, 142, 140, 47, 47, 47, 38, 38, 38, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 38, 201, 201, 201, 194, 142, 142, 140, 140, 47, 38, 38, 38, 38, 13, 6, 6, 4, 4, 38, 38] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 745 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113599 none CS(=O)(=O)NCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 68, 88, 88, 25, 23, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 24, 24, 26, 26, 26, 26, 7, 7, 1, 88, 88, 88, 68, 25, 25, 23, 23, 5, 1, 1, 1, 1, 7, 24, 24, 24, 24, 1, 1] 201 rigid atoms, others: [45, 35, 36, 37, 38, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 408 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113599 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113599/1 /scratch/stefan/7770410/working/building/REAL300020113599 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 808) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/808 `/scratch/stefan/7770410/working/3D/808' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)NCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113599.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113599/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113599 none CS(=O)(=O)NCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [151, 127, 151, 151, 55, 49, 12, 12, 12, 7, 7, 7, 1, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 1, 1, 7, 151, 151, 151, 127, 55, 55, 49, 49, 12, 7, 7, 7, 7, 1, 6, 6, 6, 6, 7, 7] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 587 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113599 none CS(=O)(=O)NCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 194, 201, 201, 142, 140, 46, 46, 46, 37, 37, 37, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 37, 201, 201, 201, 194, 142, 142, 140, 140, 46, 37, 37, 37, 37, 12, 6, 6, 4, 4, 37, 37] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 750 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113599 none CS(=O)(=O)NCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 67, 88, 88, 25, 23, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 24, 24, 26, 26, 26, 26, 7, 7, 1, 88, 88, 88, 67, 25, 25, 23, 23, 5, 1, 1, 1, 1, 7, 24, 24, 24, 24, 1, 1] 201 rigid atoms, others: [45, 35, 36, 37, 38, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 412 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113599 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113599 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113599/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113599/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113599 Building REAL300020113600 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113600' /scratch/stefan/7770410/working/building/REAL300020113600 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113600 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113600/0 /scratch/stefan/7770410/working/building/REAL300020113600 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/809 `/scratch/stefan/7770410/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)S(C)(=O)=O) `REAL300020113600.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113600 none CN(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 106, 39, 39, 39, 12, 12, 12, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 12, 133, 133, 133, 133, 133, 133, 133, 106, 106, 39, 12, 12, 12, 12, 1, 6, 6, 8, 8, 12, 12, 133, 133, 133] 201 rigid atoms, others: [36, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 493 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113600 none CN(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 179, 82, 82, 82, 40, 40, 40, 8, 8, 8, 5, 2, 1, 1, 1, 1, 1, 1, 8, 8, 40, 201, 201, 201, 201, 201, 201, 201, 179, 179, 82, 40, 40, 40, 40, 8, 5, 5, 2, 2, 40, 40, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 775 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113600 none CN(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 31, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 30, 44, 44, 44, 44, 44, 12, 12, 1, 51, 52, 52, 52, 51, 51, 51, 31, 31, 6, 1, 1, 1, 1, 12, 30, 30, 44, 44, 1, 1, 52, 52, 52] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 42, 21, 41] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 350 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113600 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113600/1 /scratch/stefan/7770410/working/building/REAL300020113600 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 810) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/810 `/scratch/stefan/7770410/working/3D/810' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)S(C)(=O)=O) `REAL300020113600.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113600 none CN(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [134, 107, 39, 39, 39, 12, 12, 12, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 12, 134, 134, 134, 134, 134, 134, 134, 107, 107, 39, 12, 12, 12, 12, 1, 6, 6, 8, 8, 12, 12, 134, 134, 134] 201 rigid atoms, others: [36, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 496 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113600 none CN(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 178, 82, 82, 82, 40, 40, 40, 8, 8, 8, 5, 2, 1, 1, 1, 1, 1, 1, 8, 8, 40, 201, 201, 201, 201, 201, 201, 201, 178, 178, 82, 40, 40, 40, 40, 8, 5, 5, 2, 2, 40, 40, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 771 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113600 none CN(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 31, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 30, 44, 44, 44, 44, 44, 12, 12, 1, 52, 53, 53, 53, 52, 52, 52, 31, 31, 6, 1, 1, 1, 1, 12, 30, 30, 44, 44, 1, 1, 53, 53, 53] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 42, 21, 41] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 354 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113600 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113600 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113600/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113600/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113600 Building REAL300020113601 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113601' /scratch/stefan/7770410/working/building/REAL300020113601 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113601 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113601/0 /scratch/stefan/7770410/working/building/REAL300020113601 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/811 `/scratch/stefan/7770410/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(=O)C1CC1) `REAL300020113601.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113601 none CN(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 67, 23, 23, 23, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 92, 119, 119, 164, 164, 92, 92, 92, 67, 67, 23, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7, 164, 164, 164, 164, 164] 201 rigid atoms, others: [37, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 642 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113601 none CN(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 115, 52, 52, 52, 35, 35, 35, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 35, 127, 148, 148, 201, 201, 127, 127, 127, 115, 115, 52, 35, 35, 35, 35, 9, 4, 4, 2, 2, 35, 35, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 776 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113601 none CN(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 20, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 19, 31, 31, 31, 31, 31, 7, 7, 1, 32, 46, 46, 67, 67, 32, 32, 32, 20, 20, 5, 1, 1, 1, 1, 7, 19, 19, 31, 31, 1, 1, 67, 67, 67, 67, 67] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 42, 43, 21] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48]) total number of confs: 381 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113601 none CN(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 6, 8, 20, 38, 38, 38, 67, 67, 67, 164, 164, 164, 188, 201, 201, 201, 201, 201, 164, 164, 67, 1, 6, 1, 1, 1, 8, 8, 8, 20, 20, 38, 67, 67, 67, 67, 164, 188, 188, 201, 201, 67, 67, 1, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 48, 22, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 585 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113601 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113601/1 /scratch/stefan/7770410/working/building/REAL300020113601 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 812) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/812 `/scratch/stefan/7770410/working/3D/812' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(=O)C1CC1) `REAL300020113601.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113601 none CN(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 67, 23, 23, 23, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 92, 119, 119, 165, 165, 92, 92, 92, 67, 67, 23, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7, 165, 165, 165, 165, 165] 201 rigid atoms, others: [37, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 646 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113601 none CN(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 116, 53, 53, 53, 35, 35, 35, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 35, 127, 148, 148, 201, 201, 127, 127, 127, 116, 116, 53, 35, 35, 35, 35, 9, 4, 4, 2, 2, 35, 35, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 776 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113601 none CN(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 20, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 18, 30, 30, 30, 30, 30, 7, 7, 1, 32, 46, 46, 68, 68, 32, 32, 32, 20, 20, 5, 1, 1, 1, 1, 7, 18, 18, 30, 30, 1, 1, 68, 68, 68, 68, 68] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 42, 43, 21] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48]) total number of confs: 382 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113601 none CN(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 6, 9, 21, 39, 39, 39, 68, 68, 68, 165, 165, 165, 188, 201, 201, 201, 201, 201, 165, 165, 68, 1, 6, 1, 1, 1, 9, 9, 9, 21, 21, 39, 68, 68, 68, 68, 165, 188, 188, 201, 201, 68, 68, 1, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 48, 22, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 586 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113601 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113601 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113601/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113601/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113601 Building REAL300020113602 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113602' /scratch/stefan/7770410/working/building/REAL300020113602 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113602 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113602/0 /scratch/stefan/7770410/working/building/REAL300020113602 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/813 `/scratch/stefan/7770410/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113602.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113602 none COCC(=O)N(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 199, 118, 67, 118, 45, 67, 17, 17, 17, 7, 7, 7, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 7, 200, 200, 200, 199, 199, 67, 67, 67, 45, 45, 17, 7, 7, 7, 7, 1, 3, 3, 3, 3, 7, 7] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 901 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113602 none COCC(=O)N(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 115, 56, 115, 56, 56, 18, 18, 18, 13, 13, 13, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 201, 201, 201, 201, 201, 56, 56, 56, 56, 56, 18, 13, 13, 13, 13, 3, 3, 3, 1, 1, 13, 13] 201 rigid atoms, others: [45, 46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 866 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113602 none COCC(=O)N(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 95, 50, 25, 50, 14, 25, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13, 13, 13, 7, 7, 1, 102, 102, 102, 95, 95, 25, 25, 25, 14, 14, 5, 1, 1, 1, 1, 7, 13, 13, 13, 13, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 470 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113602 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113602/1 /scratch/stefan/7770410/working/building/REAL300020113602 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 814) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/814 `/scratch/stefan/7770410/working/3D/814' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113602.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113602 none COCC(=O)N(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 199, 118, 67, 118, 45, 67, 17, 17, 17, 7, 7, 7, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 7, 200, 200, 200, 199, 199, 67, 67, 67, 45, 45, 17, 7, 7, 7, 7, 1, 3, 3, 3, 3, 7, 7] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 901 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113602 none COCC(=O)N(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 115, 56, 115, 56, 56, 18, 18, 18, 13, 13, 13, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 201, 201, 201, 201, 201, 56, 56, 56, 56, 56, 18, 13, 13, 13, 13, 3, 3, 3, 1, 1, 13, 13] 201 rigid atoms, others: [45, 46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 866 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113602 none COCC(=O)N(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 95, 50, 25, 50, 14, 25, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13, 13, 13, 7, 7, 1, 102, 102, 102, 95, 95, 25, 25, 25, 14, 14, 5, 1, 1, 1, 1, 7, 13, 13, 13, 13, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 470 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113602 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113602 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113602/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113602/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113602 Building REAL300020113603 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113603' /scratch/stefan/7770410/working/building/REAL300020113603 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113603 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113603/0 /scratch/stefan/7770410/working/building/REAL300020113603 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/815 `/scratch/stefan/7770410/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1=O) `REAL300020113603.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113603 none CN1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 43, 59, 69, 69, 69, 69, 12, 12, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 12, 43, 43, 59, 59, 1, 1, 20, 20] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45]) total number of confs: 302 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113603 none CN1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 44, 44, 44, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 1, 1, 12, 91, 91, 91, 91, 91, 91, 91, 91, 91, 44, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 91, 91] 201 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 290 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113603 none CN1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 8, 20, 20, 20, 91, 91, 91, 161, 201, 201, 201, 201, 201, 91, 91, 20, 1, 1, 1, 2, 2, 2, 1, 1, 1, 8, 20, 20, 20, 20, 91, 161, 161, 201, 201, 20, 20, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 44, 45, 23, 24, 25, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 737 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113603 none CN1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 140, 140, 140, 69, 69, 69, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 69, 201, 201, 201, 201, 201, 201, 201, 201, 201, 140, 69, 69, 69, 69, 13, 6, 6, 4, 4, 69, 69, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 595 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113603 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113603/1 /scratch/stefan/7770410/working/building/REAL300020113603 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 816) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/816 `/scratch/stefan/7770410/working/3D/816' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1=O) `REAL300020113603.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113603 none CN1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 43, 59, 69, 69, 69, 69, 12, 12, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 12, 43, 43, 59, 59, 1, 1, 20, 20] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45]) total number of confs: 302 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113603 none CN1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 44, 44, 44, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 1, 1, 12, 91, 91, 91, 91, 91, 91, 91, 91, 91, 44, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 91, 91] 201 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 290 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113603 none CN1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 8, 20, 20, 20, 91, 91, 91, 161, 201, 201, 201, 201, 201, 91, 91, 20, 1, 1, 1, 2, 2, 2, 1, 1, 1, 8, 20, 20, 20, 20, 91, 161, 161, 201, 201, 20, 20, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 44, 45, 23, 24, 25, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 737 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113603 none CN1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 140, 140, 140, 69, 69, 69, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 69, 201, 201, 201, 201, 201, 201, 201, 201, 201, 140, 69, 69, 69, 69, 13, 6, 6, 4, 4, 69, 69, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 595 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113603 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113603 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113603/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113603/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113603 Building REAL300020113604 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113604' /scratch/stefan/7770410/working/building/REAL300020113604 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113604 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113604/0 /scratch/stefan/7770410/working/building/REAL300020113604 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/817 `/scratch/stefan/7770410/working/3D/817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1=O) `REAL300020113604.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113604 none CCN1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 29, 42, 42, 42, 42, 42, 10, 10, 1, 20, 20, 20, 33, 33, 33, 33, 33, 20, 20, 20, 6, 1, 1, 1, 1, 10, 29, 29, 42, 42, 1, 1, 20, 20] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 45, 46, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 294 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113604 none CCN1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 74, 74, 74, 29, 29, 29, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 10, 74, 74, 74, 119, 119, 119, 119, 119, 74, 74, 74, 29, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 74, 74] 201 rigid atoms, others: [40, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 491 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113604 none CCN1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 9, 9, 9, 20, 20, 20, 74, 74, 74, 109, 134, 134, 134, 134, 134, 74, 74, 20, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 1, 9, 20, 20, 20, 20, 74, 109, 109, 134, 134, 20, 20, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 33, 34, 47, 48, 24, 25, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 460 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113604 none CCN1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 133, 133, 133, 82, 82, 82, 42, 42, 42, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 42, 133, 133, 133, 201, 201, 201, 201, 201, 133, 133, 133, 82, 42, 42, 42, 42, 8, 4, 4, 2, 2, 42, 42, 133, 133] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 799 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113604 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113604/1 /scratch/stefan/7770410/working/building/REAL300020113604 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 818) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/818 `/scratch/stefan/7770410/working/3D/818' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1=O) `REAL300020113604.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113604 none CCN1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 29, 42, 42, 42, 42, 42, 10, 10, 1, 20, 20, 20, 33, 33, 33, 33, 33, 20, 20, 20, 6, 1, 1, 1, 1, 10, 29, 29, 42, 42, 1, 1, 20, 20] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 45, 46, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 294 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113604 none CCN1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 74, 74, 74, 29, 29, 29, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 10, 74, 74, 74, 120, 120, 120, 120, 120, 74, 74, 74, 29, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 74, 74] 201 rigid atoms, others: [40, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 497 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113604 none CCN1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 9, 9, 9, 20, 20, 20, 74, 74, 74, 109, 133, 133, 133, 133, 133, 74, 74, 20, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 1, 9, 20, 20, 20, 20, 74, 109, 109, 133, 133, 20, 20, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 33, 34, 47, 48, 24, 25, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 454 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113604 none CCN1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 133, 133, 133, 82, 82, 82, 42, 42, 42, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 42, 133, 133, 133, 201, 201, 201, 201, 201, 133, 133, 133, 82, 42, 42, 42, 42, 8, 4, 4, 2, 2, 42, 42, 133, 133] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 799 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113604 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113604 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113604/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113604/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113604 Building REAL300020113605 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113605' /scratch/stefan/7770410/working/building/REAL300020113605 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113605 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113605/0 /scratch/stefan/7770410/working/building/REAL300020113605 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 819) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/819 `/scratch/stefan/7770410/working/3D/819' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113605.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113605 none COCC(=O)NCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [160, 143, 73, 73, 73, 71, 59, 15, 15, 15, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 160, 160, 160, 143, 143, 73, 71, 71, 59, 59, 15, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 721 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113605 none COCC(=O)NCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 102, 102, 102, 100, 85, 44, 44, 44, 34, 34, 34, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 34, 201, 201, 201, 201, 201, 102, 100, 100, 85, 85, 44, 34, 34, 34, 34, 8, 4, 4, 2, 2, 34, 34] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 917 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113605 none COCC(=O)NCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 71, 33, 33, 33, 31, 18, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 19, 31, 31, 31, 31, 31, 7, 7, 1, 82, 82, 82, 71, 71, 33, 31, 31, 18, 18, 5, 1, 1, 1, 1, 7, 19, 19, 31, 31, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 469 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113605 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113605/1 /scratch/stefan/7770410/working/building/REAL300020113605 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 820) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/820 `/scratch/stefan/7770410/working/3D/820' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113605.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113605/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113605 none COCC(=O)NCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [159, 142, 74, 74, 74, 72, 60, 15, 15, 15, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 159, 159, 159, 142, 142, 74, 72, 72, 60, 60, 15, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 715 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113605 none COCC(=O)NCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 102, 102, 102, 100, 84, 44, 44, 44, 34, 34, 34, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 34, 201, 201, 201, 201, 201, 102, 100, 100, 84, 84, 44, 34, 34, 34, 34, 8, 4, 4, 2, 2, 34, 34] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 920 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113605 none COCC(=O)NCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 71, 33, 33, 33, 31, 18, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 19, 31, 31, 31, 31, 31, 7, 7, 1, 82, 82, 82, 71, 71, 33, 31, 31, 18, 18, 5, 1, 1, 1, 1, 7, 19, 19, 31, 31, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 469 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113605 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113605 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113605/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113605/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113605 Building REAL300020113606 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113606' /scratch/stefan/7770410/working/building/REAL300020113606 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113606 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113606/0 /scratch/stefan/7770410/working/building/REAL300020113606 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/821 `/scratch/stefan/7770410/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCNC(=O)C1CC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113606.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113606 none O=C(CCCNC(=O)C1CC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 16, 22, 22, 35, 35, 35, 71, 71, 1, 1, 1, 1, 1, 7, 7, 7, 20, 20, 20, 20, 20, 20, 7, 7, 1, 16, 16, 22, 22, 22, 22, 35, 71, 71, 71, 71, 71, 4, 1, 1, 1, 1, 7, 20, 20, 20, 20, 1, 1] 201 rigid atoms, others: [43, 41, 42, 11, 12, 13, 14, 15, 50, 51, 27, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 323 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113606 none O=C(CCCNC(=O)C1CC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 46, 62, 62, 81, 81, 81, 137, 137, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 7, 46, 46, 62, 62, 62, 62, 81, 137, 137, 137, 137, 137, 13, 7, 7, 7, 7, 1, 5, 5, 5, 5, 7, 7] 201 rigid atoms, others: [45, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 556 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113606 none O=C(CCCNC(=O)C1CC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 27, 15, 21, 7, 7, 1, 7, 1, 1, 1, 48, 48, 71, 71, 71, 137, 137, 137, 201, 201, 201, 201, 201, 201, 137, 137, 71, 23, 23, 21, 21, 21, 21, 7, 1, 1, 1, 1, 1, 48, 71, 71, 71, 71, 137, 201, 201, 201, 201, 71, 71] 201 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 38] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 695 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113606 none O=C(CCCNC(=O)C1CC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 76, 85, 85, 138, 138, 138, 201, 201, 23, 23, 23, 7, 7, 7, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 23, 76, 76, 85, 85, 85, 85, 138, 201, 201, 201, 201, 201, 41, 23, 23, 23, 23, 7, 2, 2, 2, 2, 23, 23] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 783 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113606 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113606/1 /scratch/stefan/7770410/working/building/REAL300020113606 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 822) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/822 `/scratch/stefan/7770410/working/3D/822' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCNC(=O)C1CC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113606.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113606 none O=C(CCCNC(=O)C1CC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 16, 22, 22, 35, 35, 35, 71, 71, 1, 1, 1, 1, 1, 7, 7, 7, 20, 20, 20, 20, 20, 20, 7, 7, 1, 16, 16, 22, 22, 22, 22, 35, 71, 71, 71, 71, 71, 4, 1, 1, 1, 1, 7, 20, 20, 20, 20, 1, 1] 201 rigid atoms, others: [43, 41, 42, 11, 12, 13, 14, 15, 50, 51, 27, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 323 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113606 none O=C(CCCNC(=O)C1CC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 45, 61, 61, 80, 80, 80, 137, 137, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 7, 45, 45, 61, 61, 61, 61, 80, 137, 137, 137, 137, 137, 13, 7, 7, 7, 7, 1, 5, 5, 5, 5, 7, 7] 201 rigid atoms, others: [45, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 557 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113606 none O=C(CCCNC(=O)C1CC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 27, 15, 21, 7, 7, 1, 7, 1, 1, 1, 48, 48, 71, 71, 71, 137, 137, 137, 201, 201, 201, 201, 201, 201, 137, 137, 71, 23, 23, 21, 21, 21, 21, 7, 1, 1, 1, 1, 1, 48, 71, 71, 71, 71, 137, 201, 201, 201, 201, 71, 71] 201 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 38] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 695 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113606 none O=C(CCCNC(=O)C1CC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 76, 85, 85, 138, 138, 138, 201, 201, 23, 23, 23, 7, 7, 7, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 23, 76, 76, 85, 85, 85, 85, 138, 201, 201, 201, 201, 201, 41, 23, 23, 23, 23, 7, 2, 2, 2, 2, 23, 23] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 783 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113606 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113606 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113606/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113606/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113606 Building REAL300020113607 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113607' /scratch/stefan/7770410/working/building/REAL300020113607 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113607 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113607/0 /scratch/stefan/7770410/working/building/REAL300020113607 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 823) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/823 `/scratch/stefan/7770410/working/3D/823' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020113607.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113607 none CCCOC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 31, 31, 11, 11, 11, 11, 11, 4, 4, 4, 1, 1, 1, 1, 1, 7, 7, 7, 20, 31, 31, 31, 31, 31, 7, 7, 1, 11, 44, 44, 44, 44, 44, 31, 31, 11, 11, 11, 4, 1, 1, 1, 1, 7, 20, 20, 31, 31, 1, 1, 11] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 51]) total number of confs: 252 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113607 none CCCOC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 95, 95, 46, 46, 46, 46, 46, 14, 14, 14, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 46, 109, 109, 109, 109, 109, 95, 95, 46, 46, 46, 14, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7, 46] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 281 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113607 none CCCOC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 46, 46, 46, 83, 107, 107, 107, 107, 107, 46, 46, 11, 1, 14, 14, 14, 14, 14, 6, 6, 1, 1, 1, 5, 11, 11, 11, 11, 46, 83, 83, 107, 107, 11, 11, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 51, 36, 38, 28, 37] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 437 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113607 none CCCOC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 108, 108, 108, 108, 108, 40, 40, 40, 30, 30, 30, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 30, 108, 201, 201, 201, 201, 201, 201, 201, 108, 108, 108, 40, 30, 30, 30, 30, 9, 4, 4, 2, 2, 30, 30, 108] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 365 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113607 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113607/1 /scratch/stefan/7770410/working/building/REAL300020113607 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 824) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/824 `/scratch/stefan/7770410/working/3D/824' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020113607.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113607 none CCCOC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 30, 30, 10, 10, 10, 10, 10, 4, 4, 4, 1, 1, 1, 1, 1, 7, 7, 7, 20, 31, 31, 31, 31, 31, 7, 7, 1, 10, 42, 42, 42, 42, 42, 30, 30, 10, 10, 10, 4, 1, 1, 1, 1, 7, 20, 20, 31, 31, 1, 1, 10] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 51]) total number of confs: 244 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113607 none CCCOC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 95, 95, 45, 45, 45, 45, 45, 14, 14, 14, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 45, 108, 108, 108, 108, 108, 95, 95, 45, 45, 45, 14, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7, 45] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 275 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113607 none CCCOC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 45, 45, 45, 82, 107, 107, 107, 107, 107, 45, 45, 10, 1, 13, 13, 13, 13, 13, 6, 6, 1, 1, 1, 5, 10, 10, 10, 10, 45, 82, 82, 107, 107, 10, 10, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 51, 36, 38, 28, 37] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 438 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113607 none CCCOC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 106, 106, 106, 106, 106, 38, 38, 38, 29, 29, 29, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 29, 106, 201, 201, 201, 201, 201, 201, 201, 106, 106, 106, 38, 29, 29, 29, 29, 8, 4, 4, 2, 2, 29, 29, 106] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 365 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113607 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113607 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113607/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113607/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113607 Building REAL300020113608 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113608' /scratch/stefan/7770410/working/building/REAL300020113608 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113608 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113608/0 /scratch/stefan/7770410/working/building/REAL300020113608 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/825 `/scratch/stefan/7770410/working/3D/825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCN1C=CC=CC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113608.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113608 none O=C(CCN1C=CC=CC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 22, 26, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 9, 9, 9, 24, 36, 36, 36, 36, 36, 9, 9, 1, 22, 22, 26, 26, 28, 28, 28, 28, 5, 1, 1, 1, 1, 9, 24, 24, 36, 36, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 246 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113608 none O=C(CCN1C=CC=CC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 89, 100, 104, 104, 104, 104, 104, 104, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 9, 89, 89, 100, 100, 104, 104, 104, 104, 23, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 406 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113608 none O=C(CCN1C=CC=CC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 28, 28, 28, 104, 104, 104, 164, 201, 201, 201, 201, 201, 104, 104, 28, 5, 5, 3, 3, 1, 1, 1, 1, 17, 28, 28, 28, 28, 104, 164, 164, 201, 201, 28, 28] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 35] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 740 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113608 none O=C(CCN1C=CC=CC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 194, 198, 201, 201, 201, 201, 201, 201, 38, 38, 38, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 38, 194, 194, 198, 198, 201, 201, 201, 201, 71, 38, 38, 38, 38, 9, 4, 4, 2, 2, 38, 38] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 722 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113608 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113608/1 /scratch/stefan/7770410/working/building/REAL300020113608 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 826) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/826 `/scratch/stefan/7770410/working/3D/826' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCN1C=CC=CC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113608.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113608 none O=C(CCN1C=CC=CC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 22, 26, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 9, 9, 9, 24, 36, 36, 36, 36, 36, 9, 9, 1, 22, 22, 26, 26, 28, 28, 28, 28, 5, 1, 1, 1, 1, 9, 24, 24, 36, 36, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 246 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113608 none O=C(CCN1C=CC=CC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 89, 100, 104, 104, 104, 104, 104, 104, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 9, 89, 89, 100, 100, 104, 104, 104, 104, 23, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 406 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113608 none O=C(CCN1C=CC=CC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 28, 28, 28, 104, 104, 104, 164, 201, 201, 201, 201, 201, 104, 104, 28, 5, 5, 3, 3, 1, 1, 1, 1, 17, 28, 28, 28, 28, 104, 164, 164, 201, 201, 28, 28] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 35] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 740 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113608 none O=C(CCN1C=CC=CC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 194, 198, 201, 201, 201, 201, 201, 201, 37, 37, 37, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 37, 194, 194, 198, 198, 201, 201, 201, 201, 69, 37, 37, 37, 37, 9, 4, 4, 2, 2, 37, 37] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 721 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113608 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113608 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113608/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113608/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113608 Building REAL300020113609 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113609' /scratch/stefan/7770410/working/building/REAL300020113609 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113609 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113609/0 /scratch/stefan/7770410/working/building/REAL300020113609 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/827 `/scratch/stefan/7770410/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)N1C(=O)CCC1=O) `REAL300020113609.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113609 none CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)N1C(=O)CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 11, 5, 5, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 36, 36, 36, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 114, 114, 114, 114, 114, 114, 114, 114, 114, 114, 114, 36, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 114, 114, 114, 114] 201 rigid atoms, others: [37, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 441 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113609 none CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)N1C(=O)CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 11, 5, 5, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 122, 122, 122, 60, 60, 60, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 60, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 122, 60, 60, 60, 60, 11, 6, 6, 4, 4, 60, 60, 201, 201, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 759 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113609 none CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)N1C(=O)CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 11, 5, 5, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 34, 49, 60, 60, 60, 60, 11, 11, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 34, 34, 49, 49, 1, 1, 22, 22, 22, 22] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 42, 43, 20, 36] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113609 none CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)N1C(=O)CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 11, 5, 5, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 9, 9, 10, 25, 25, 25, 116, 116, 116, 174, 201, 201, 201, 201, 201, 116, 116, 25, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 2, 9, 25, 25, 25, 25, 116, 174, 174, 201, 201, 25, 25, 1, 1, 1, 1] 201 rigid atoms, others: [1, 44, 45, 46, 47, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 661 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113609 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113609/1 /scratch/stefan/7770410/working/building/REAL300020113609 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 828) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/828 `/scratch/stefan/7770410/working/3D/828' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)N1C(=O)CCC1=O) `REAL300020113609.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113609 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)N1C(=O)CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 11, 5, 5, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 36, 36, 36, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 36, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 112, 112, 112, 112] 201 rigid atoms, others: [37, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 435 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113609 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)N1C(=O)CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 11, 5, 5, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 123, 123, 123, 60, 60, 60, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 60, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 123, 60, 60, 60, 60, 11, 6, 6, 4, 4, 60, 60, 201, 201, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 760 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113609 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)N1C(=O)CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 11, 5, 5, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 34, 49, 60, 60, 60, 60, 11, 11, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 34, 34, 49, 49, 1, 1, 22, 22, 22, 22] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 42, 43, 20, 36] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113609 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)N1C(=O)CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 11, 5, 5, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 9, 9, 10, 25, 25, 25, 115, 115, 115, 173, 201, 201, 201, 201, 201, 115, 115, 25, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 2, 9, 25, 25, 25, 25, 115, 173, 173, 201, 201, 25, 25, 1, 1, 1, 1] 201 rigid atoms, others: [1, 44, 45, 46, 47, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 665 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113609 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113609 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113609/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113609/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113609 Building REAL300020113610 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113610' /scratch/stefan/7770410/working/building/REAL300020113610 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113610 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113610/0 /scratch/stefan/7770410/working/building/REAL300020113610 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/829 `/scratch/stefan/7770410/working/3D/829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1) `REAL300020113610.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113610 none CCOC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 24, 17, 17, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 38, 52, 57, 57, 57, 57, 11, 11, 1, 17, 17, 30, 30, 30, 30, 30, 17, 17, 6, 1, 1, 1, 1, 11, 38, 38, 52, 52, 1, 1, 17] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47]) total number of confs: 286 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113610 none CCOC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 98, 79, 79, 79, 79, 32, 32, 32, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 79, 79, 106, 106, 106, 106, 106, 79, 79, 32, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 79] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 277 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113610 none CCOC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 79, 79, 79, 153, 200, 200, 200, 200, 200, 79, 79, 17, 1, 1, 8, 8, 8, 7, 7, 1, 1, 5, 17, 17, 17, 17, 79, 153, 153, 200, 200, 17, 17, 1] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 47, 26, 27] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 794 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113610 none CCOC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 200, 200, 200, 200, 117, 117, 117, 58, 58, 58, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 58, 200, 200, 201, 201, 201, 201, 201, 200, 200, 117, 58, 58, 58, 58, 13, 6, 6, 4, 4, 58, 58, 200] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 468 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113610 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113610/1 /scratch/stefan/7770410/working/building/REAL300020113610 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 830) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/830 `/scratch/stefan/7770410/working/3D/830' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1) `REAL300020113610.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113610 none CCOC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 24, 17, 17, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 38, 52, 56, 56, 56, 56, 11, 11, 1, 17, 17, 30, 30, 30, 30, 30, 17, 17, 6, 1, 1, 1, 1, 11, 38, 38, 52, 52, 1, 1, 17] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47]) total number of confs: 284 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113610 none CCOC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 98, 79, 79, 79, 79, 32, 32, 32, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 79, 79, 106, 106, 106, 106, 106, 79, 79, 32, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 79] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 277 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113610 none CCOC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 79, 79, 79, 153, 200, 200, 200, 200, 200, 79, 79, 17, 1, 1, 8, 8, 8, 7, 7, 1, 1, 5, 17, 17, 17, 17, 79, 153, 153, 200, 200, 17, 17, 1] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 47, 26, 27] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 788 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113610 none CCOC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 200, 200, 200, 200, 117, 117, 117, 59, 59, 59, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 59, 200, 200, 201, 201, 201, 201, 201, 200, 200, 117, 59, 59, 59, 59, 13, 6, 6, 4, 4, 59, 59, 200] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 467 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113610 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113610 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113610/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113610/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113610 Building REAL300020113611 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113611' /scratch/stefan/7770410/working/building/REAL300020113611 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113611 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113611/0 /scratch/stefan/7770410/working/building/REAL300020113611 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/831 `/scratch/stefan/7770410/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1OCCO2) `REAL300020113611.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113611 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1OCCO2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 11, 40, 95, 95, 95, 95, 95, 95, 95, 95, 95, 40, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 95, 95, 95, 95, 95, 95, 95] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 225 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113611 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1OCCO2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [154, 154, 81, 81, 81, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 81, 154, 201, 201, 201, 201, 201, 201, 201, 201, 201, 154, 81, 81, 81, 81, 15, 6, 6, 4, 4, 81, 81, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 524 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113611 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1OCCO2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 50, 67, 81, 81, 81, 81, 11, 11, 1, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 11, 50, 50, 67, 67, 1, 1, 20, 20, 20, 20, 20, 20, 20] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 320 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113611 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1OCCO2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 20, 20, 20, 95, 95, 95, 173, 201, 201, 201, 201, 201, 95, 95, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 20, 20, 20, 20, 95, 173, 173, 201, 201, 20, 20, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 47, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 704 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113611 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113611/1 /scratch/stefan/7770410/working/building/REAL300020113611 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 832) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/832 `/scratch/stefan/7770410/working/3D/832' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1OCCO2) `REAL300020113611.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113611 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1OCCO2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 11, 39, 94, 94, 94, 94, 94, 94, 94, 94, 94, 39, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 94, 94, 94, 94, 94, 94, 94] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 223 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113611 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1OCCO2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [153, 153, 81, 81, 81, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 81, 153, 201, 201, 201, 201, 201, 201, 201, 201, 201, 153, 81, 81, 81, 81, 15, 6, 6, 4, 4, 81, 81, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 524 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113611 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1OCCO2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 50, 67, 81, 81, 81, 81, 11, 11, 1, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 11, 50, 50, 67, 67, 1, 1, 20, 20, 20, 20, 20, 20, 20] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 320 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113611 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1OCCO2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 20, 20, 20, 94, 94, 94, 173, 201, 201, 201, 201, 201, 94, 94, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 20, 20, 20, 20, 94, 173, 173, 201, 201, 20, 20, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 47, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 709 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113611 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113611 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113611/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113611/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113611 Building REAL300020113612 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113612' /scratch/stefan/7770410/working/building/REAL300020113612 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113612 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113612/0 /scratch/stefan/7770410/working/building/REAL300020113612 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/833 `/scratch/stefan/7770410/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=NN1C(C)(C)C) `REAL300020113612.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113612 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=NN1C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 27, 35, 41, 41, 41, 41, 7, 7, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 7, 27, 27, 35, 35, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27] 109 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 42, 43, 21] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 184 number of broken/clashed sets: 109 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113612 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=NN1C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 21, 21, 21, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 7, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 21, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58] 109 rigid atoms, others: [37, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 152 number of broken/clashed sets: 109 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113612 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=NN1C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 8, 8, 8, 27, 27, 27, 58, 58, 58, 93, 109, 109, 109, 109, 109, 58, 58, 27, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 8, 27, 27, 27, 27, 58, 93, 93, 109, 109, 27, 27, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 109 rigid atoms, others: [0, 1, 2, 3, 44, 22, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 396 number of broken/clashed sets: 109 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113612 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=NN1C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 72, 72, 72, 44, 44, 44, 18, 18, 18, 7, 4, 1, 1, 1, 1, 1, 1, 18, 18, 44, 109, 109, 109, 109, 109, 109, 109, 109, 109, 109, 72, 44, 44, 44, 44, 18, 7, 7, 4, 4, 44, 44, 109, 109, 109, 109, 109, 109, 109, 109, 109, 109] 109 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 268 number of broken/clashed sets: 109 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113612 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113612/1 /scratch/stefan/7770410/working/building/REAL300020113612 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 834) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/834 `/scratch/stefan/7770410/working/3D/834' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=NN1C(C)(C)C) `REAL300020113612.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113612 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=NN1C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 26, 34, 40, 40, 40, 40, 7, 7, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 7, 26, 26, 34, 34, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27] 108 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 42, 43, 21] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 181 number of broken/clashed sets: 108 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113612 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=NN1C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 21, 21, 21, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 7, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 21, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58] 108 rigid atoms, others: [37, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 152 number of broken/clashed sets: 108 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113612 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=NN1C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 8, 8, 8, 27, 27, 27, 58, 58, 58, 92, 108, 108, 108, 108, 108, 58, 58, 27, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 8, 27, 27, 27, 27, 58, 92, 92, 108, 108, 27, 27, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 108 rigid atoms, others: [0, 1, 2, 3, 44, 22, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 393 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113612 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=NN1C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 72, 72, 72, 44, 44, 44, 18, 18, 18, 7, 4, 1, 1, 1, 1, 1, 1, 18, 18, 44, 109, 109, 109, 109, 109, 109, 109, 109, 109, 109, 72, 44, 44, 44, 44, 18, 7, 7, 4, 4, 44, 44, 109, 109, 109, 109, 109, 109, 109, 109, 109, 109] 109 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 268 number of broken/clashed sets: 109 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113612 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113612 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113612/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113612/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113612 Building REAL300020113613 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113613' /scratch/stefan/7770410/working/building/REAL300020113613 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113613 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113613/0 /scratch/stefan/7770410/working/building/REAL300020113613 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/835 `/scratch/stefan/7770410/working/3D/835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113613.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113613 none CNC(=O)NCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 110, 110, 110, 108, 23, 23, 23, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 112, 112, 112, 112, 110, 108, 108, 23, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 404 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113613 none CNC(=O)NCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 200, 73, 73, 73, 39, 39, 39, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 39, 201, 201, 201, 201, 201, 200, 200, 73, 39, 39, 39, 39, 8, 4, 4, 2, 2, 39, 39] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 727 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113613 none CNC(=O)NCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 36, 36, 36, 30, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 24, 37, 37, 37, 37, 37, 8, 8, 1, 39, 39, 39, 39, 36, 30, 30, 5, 1, 1, 1, 1, 8, 24, 24, 37, 37, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 287 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113613 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113613/1 /scratch/stefan/7770410/working/building/REAL300020113613 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 836) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/836 `/scratch/stefan/7770410/working/3D/836' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113613.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113613 none CNC(=O)NCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 110, 110, 110, 108, 23, 23, 23, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 112, 112, 112, 112, 110, 108, 108, 23, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 404 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113613 none CNC(=O)NCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 200, 73, 73, 73, 38, 38, 38, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 38, 201, 201, 201, 201, 201, 200, 200, 73, 38, 38, 38, 38, 7, 4, 4, 2, 2, 38, 38] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 729 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113613 none CNC(=O)NCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 36, 36, 36, 30, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 24, 37, 37, 37, 37, 37, 8, 8, 1, 39, 39, 39, 39, 36, 30, 30, 5, 1, 1, 1, 1, 8, 24, 24, 37, 37, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 287 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113613 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113613 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113613/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113613/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113613 Building REAL300020113614 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113614' /scratch/stefan/7770410/working/building/REAL300020113614 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113614 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113614/0 /scratch/stefan/7770410/working/building/REAL300020113614 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 837) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/837 `/scratch/stefan/7770410/working/3D/837' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1) `REAL300020113614.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113614 none CC(C)OC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 18, 26, 13, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 45, 47, 47, 47, 47, 11, 11, 1, 13, 13, 26, 26, 26, 26, 26, 26, 26, 13, 13, 6, 1, 1, 1, 1, 11, 31, 31, 45, 45, 1, 1, 13] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50]) total number of confs: 261 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113614 none CC(C)OC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 82, 109, 71, 71, 71, 71, 28, 28, 28, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 71, 71, 109, 109, 109, 109, 109, 109, 109, 71, 71, 28, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 71] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 349 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113614 none CC(C)OC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 6, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 71, 71, 71, 141, 189, 192, 192, 192, 192, 71, 71, 13, 1, 1, 6, 6, 6, 6, 6, 6, 6, 1, 1, 5, 13, 13, 13, 13, 71, 141, 141, 189, 189, 13, 13, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 50, 36, 27, 28, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 736 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113614 none CC(C)OC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 196, 196, 196, 196, 84, 84, 84, 44, 44, 44, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 44, 196, 196, 201, 201, 201, 201, 201, 201, 201, 196, 196, 84, 44, 44, 44, 44, 9, 5, 5, 3, 3, 44, 44, 196] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 426 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113614 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113614/1 /scratch/stefan/7770410/working/building/REAL300020113614 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 838) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/838 `/scratch/stefan/7770410/working/3D/838' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1) `REAL300020113614.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113614 none CC(C)OC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 18, 27, 13, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 45, 47, 47, 47, 47, 11, 11, 1, 13, 13, 27, 27, 27, 27, 27, 27, 27, 13, 13, 6, 1, 1, 1, 1, 11, 31, 31, 45, 45, 1, 1, 13] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50]) total number of confs: 267 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113614 none CC(C)OC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 81, 109, 71, 71, 71, 71, 28, 28, 28, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 71, 71, 109, 109, 109, 109, 109, 109, 109, 71, 71, 28, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 71] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 353 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113614 none CC(C)OC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 6, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 71, 71, 71, 142, 190, 193, 193, 193, 193, 71, 71, 13, 1, 1, 6, 6, 6, 6, 6, 6, 6, 1, 1, 5, 13, 13, 13, 13, 71, 142, 142, 190, 190, 13, 13, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 50, 36, 27, 28, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 739 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113614 none CC(C)OC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 196, 196, 196, 196, 84, 84, 84, 44, 44, 44, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 44, 196, 196, 201, 201, 201, 201, 201, 201, 201, 196, 196, 84, 44, 44, 44, 44, 9, 5, 5, 3, 3, 44, 44, 196] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 426 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113614 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113614 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113614/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113614/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113614 Building REAL300020113615 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113615' /scratch/stefan/7770410/working/building/REAL300020113615 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113615 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113615/0 /scratch/stefan/7770410/working/building/REAL300020113615 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/839 `/scratch/stefan/7770410/working/3D/839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1CCCS1(=O)=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113615.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113615 none O=C(CN1CCCS1(=O)=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 14, 11, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 29, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 12, 12, 12, 33, 47, 48, 48, 48, 48, 12, 12, 1, 29, 29, 39, 39, 39, 39, 39, 39, 6, 1, 1, 1, 1, 12, 33, 33, 47, 47, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 302 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113615 none O=C(CN1CCCS1(=O)=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 14, 11, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 113, 130, 130, 130, 130, 130, 130, 12, 12, 12, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 12, 113, 113, 130, 130, 130, 130, 130, 130, 37, 12, 12, 12, 12, 1, 6, 6, 8, 8, 12, 12] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 457 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113615 none O=C(CN1CCCS1(=O)=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 14, 11, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 39, 39, 39, 130, 130, 130, 177, 201, 201, 201, 201, 201, 130, 130, 39, 7, 7, 1, 1, 1, 1, 1, 1, 18, 39, 39, 39, 39, 130, 177, 177, 201, 201, 39, 39] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 644 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113615 none O=C(CN1CCCS1(=O)=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 14, 11, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 199, 201, 201, 201, 201, 201, 201, 49, 49, 49, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 49, 199, 199, 201, 201, 201, 201, 201, 201, 105, 49, 49, 49, 49, 10, 6, 6, 4, 4, 49, 49] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 750 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113615 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113615/1 /scratch/stefan/7770410/working/building/REAL300020113615 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 840) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/840 `/scratch/stefan/7770410/working/3D/840' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1CCCS1(=O)=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113615.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113615 none O=C(CN1CCCS1(=O)=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 14, 11, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 29, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 12, 12, 12, 33, 47, 48, 48, 48, 48, 12, 12, 1, 29, 29, 39, 39, 39, 39, 39, 39, 6, 1, 1, 1, 1, 12, 33, 33, 47, 47, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 302 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113615 none O=C(CN1CCCS1(=O)=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 14, 11, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 113, 130, 130, 130, 130, 130, 130, 12, 12, 12, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 12, 113, 113, 130, 130, 130, 130, 130, 130, 37, 12, 12, 12, 12, 1, 6, 6, 8, 8, 12, 12] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 457 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113615 none O=C(CN1CCCS1(=O)=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 14, 11, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 39, 39, 39, 130, 130, 130, 177, 201, 201, 201, 201, 201, 130, 130, 39, 7, 7, 1, 1, 1, 1, 1, 1, 18, 39, 39, 39, 39, 130, 177, 177, 201, 201, 39, 39] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 641 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113615 none O=C(CN1CCCS1(=O)=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 14, 11, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 199, 201, 201, 201, 201, 201, 201, 49, 49, 49, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 49, 199, 199, 201, 201, 201, 201, 201, 201, 106, 49, 49, 49, 49, 10, 6, 6, 4, 4, 49, 49] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 746 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113615 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113615 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113615/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113615/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113615 Building REAL300020113616 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113616' /scratch/stefan/7770410/working/building/REAL300020113616 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113616 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113616/0 /scratch/stefan/7770410/working/building/REAL300020113616 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/841 `/scratch/stefan/7770410/working/3D/841' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C2=CC=C(F)C=C2)CC1) `REAL300020113616.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113616 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C2=CC=C(F)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 58, 152, 152, 152, 152, 152, 152, 152, 152, 152, 58, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 152, 152, 152, 152, 152, 152, 152, 152] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 457 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113616 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C2=CC=C(F)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 2, 11, 11, 30, 30, 30, 152, 152, 152, 181, 201, 201, 201, 201, 201, 152, 152, 30, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 11, 30, 30, 30, 30, 152, 181, 181, 201, 201, 30, 30, 1, 1, 1, 1, 2, 2, 2, 2] 201 rigid atoms, others: [41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48]) total number of confs: 509 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113616 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C2=CC=C(F)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 36, 36, 36, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 36, 101, 201, 201, 201, 201, 201, 201, 201, 201, 201, 101, 36, 36, 36, 36, 9, 4, 4, 2, 2, 36, 36, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 585 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113616 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C2=CC=C(F)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 26, 34, 34, 34, 34, 34, 13, 13, 1, 6, 30, 30, 30, 30, 30, 30, 30, 30, 30, 6, 1, 1, 1, 1, 13, 26, 26, 34, 34, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 195 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113616 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C2=CC=C(F)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 30, 30, 30, 152, 152, 152, 181, 201, 201, 201, 201, 201, 152, 152, 30, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 11, 30, 30, 30, 30, 152, 181, 181, 201, 201, 30, 30, 2, 2, 2, 2, 1, 1, 1, 1] 201 rigid atoms, others: [1, 45, 46, 47, 48, 19, 20, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 509 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113616 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113616/1 /scratch/stefan/7770410/working/building/REAL300020113616 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 842) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/842 `/scratch/stefan/7770410/working/3D/842' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C2=CC=C(F)C=C2)CC1) `REAL300020113616.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113616 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C2=CC=C(F)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 58, 152, 152, 152, 152, 152, 152, 152, 152, 152, 58, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 152, 152, 152, 152, 152, 152, 152, 152] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 457 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113616 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C2=CC=C(F)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 2, 11, 11, 30, 30, 30, 152, 152, 152, 181, 201, 201, 201, 201, 201, 152, 152, 30, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 11, 30, 30, 30, 30, 152, 181, 181, 201, 201, 30, 30, 1, 1, 1, 1, 2, 2, 2, 2] 201 rigid atoms, others: [41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48]) total number of confs: 509 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113616 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C2=CC=C(F)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 36, 36, 36, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 36, 101, 201, 201, 201, 201, 201, 201, 201, 201, 201, 101, 36, 36, 36, 36, 8, 4, 4, 2, 2, 36, 36, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 587 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113616 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C2=CC=C(F)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 26, 34, 34, 34, 34, 34, 13, 13, 1, 6, 30, 30, 30, 30, 30, 30, 30, 30, 30, 6, 1, 1, 1, 1, 13, 26, 26, 34, 34, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 195 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113616 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C2=CC=C(F)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 30, 30, 30, 152, 152, 152, 181, 201, 201, 201, 201, 201, 152, 152, 30, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 11, 30, 30, 30, 30, 152, 181, 181, 201, 201, 30, 30, 2, 2, 2, 2, 1, 1, 1, 1] 201 rigid atoms, others: [1, 45, 46, 47, 48, 19, 20, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 509 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113616 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113616 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113616/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113616/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113616 Building REAL300020113617 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113617' /scratch/stefan/7770410/working/building/REAL300020113617 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113617 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113617/0 /scratch/stefan/7770410/working/building/REAL300020113617 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/843 `/scratch/stefan/7770410/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(COCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1) `REAL300020113617.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113617 none CC1=CC=C(COCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 34, 48, 48, 31, 15, 13, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 20, 32, 32, 32, 32, 32, 7, 7, 1, 48, 48, 48, 48, 48, 48, 48, 31, 31, 13, 13, 5, 1, 1, 1, 1, 7, 20, 20, 32, 32, 1, 1, 48, 48] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50, 51]) total number of confs: 386 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113617 none CC1=CC=C(COCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 102, 129, 129, 88, 47, 45, 17, 17, 17, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 129, 129, 129, 129, 129, 129, 129, 88, 88, 45, 45, 17, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 129, 129] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 678 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113617 none CC1=CC=C(COCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 11, 22, 31, 31, 31, 56, 56, 56, 138, 138, 138, 186, 201, 201, 201, 201, 201, 138, 138, 56, 1, 1, 2, 2, 2, 1, 1, 4, 4, 22, 22, 31, 56, 56, 56, 56, 138, 186, 186, 201, 201, 56, 56, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 50, 51, 27, 28, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 696 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113617 none CC1=CC=C(COCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 187, 201, 201, 186, 117, 113, 51, 51, 51, 31, 31, 31, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 31, 201, 201, 201, 201, 201, 201, 201, 186, 186, 113, 113, 51, 31, 31, 31, 31, 7, 4, 4, 2, 2, 31, 31, 201, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 930 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113617 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113617/1 /scratch/stefan/7770410/working/building/REAL300020113617 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 844) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/844 `/scratch/stefan/7770410/working/3D/844' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(COCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1) `REAL300020113617.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113617 none CC1=CC=C(COCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 33, 47, 47, 30, 15, 13, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 20, 32, 32, 32, 32, 32, 7, 7, 1, 47, 47, 47, 47, 47, 47, 47, 30, 30, 13, 13, 5, 1, 1, 1, 1, 7, 20, 20, 32, 32, 1, 1, 47, 47] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50, 51]) total number of confs: 380 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113617 none CC1=CC=C(COCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 101, 130, 130, 87, 47, 45, 17, 17, 17, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 130, 130, 130, 130, 130, 130, 130, 87, 87, 45, 45, 17, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 130, 130] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 686 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113617 none CC1=CC=C(COCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 11, 22, 31, 31, 31, 56, 56, 56, 138, 138, 138, 186, 201, 201, 201, 201, 201, 138, 138, 56, 1, 1, 2, 2, 2, 1, 1, 4, 4, 22, 22, 31, 56, 56, 56, 56, 138, 186, 186, 201, 201, 56, 56, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 50, 51, 27, 28, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 696 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113617 none CC1=CC=C(COCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 187, 201, 201, 187, 118, 114, 52, 52, 52, 32, 32, 32, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 32, 201, 201, 201, 201, 201, 201, 201, 187, 187, 114, 114, 52, 32, 32, 32, 32, 7, 4, 4, 2, 2, 32, 32, 201, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 927 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113617 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113617 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113617/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113617/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113617 Building REAL300020113618 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113618' /scratch/stefan/7770410/working/building/REAL300020113618 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113618 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113618/0 /scratch/stefan/7770410/working/building/REAL300020113618 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 845) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/845 `/scratch/stefan/7770410/working/3D/845' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCC1) `REAL300020113618.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113618 none COCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 16, 11, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 32, 45, 49, 49, 49, 49, 10, 10, 1, 11, 11, 11, 11, 26, 26, 26, 16, 16, 6, 1, 1, 1, 1, 10, 32, 32, 45, 45, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 272 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113618 none COCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 76, 69, 39, 39, 39, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 10, 69, 69, 69, 69, 87, 87, 87, 76, 76, 39, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 69, 69, 69, 69, 69, 69, 69, 69] 201 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 315 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113618 none COCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 3, 3, 3, 11, 11, 11, 69, 69, 69, 154, 201, 201, 201, 201, 201, 69, 69, 11, 1, 1, 1, 1, 9, 9, 9, 5, 5, 3, 11, 11, 11, 11, 69, 154, 154, 201, 201, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 44, 45, 46, 47, 48, 49, 50, 51, 23, 24, 25, 26] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 810 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113618 none COCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 186, 132, 132, 132, 60, 60, 60, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 60, 186, 186, 186, 186, 201, 201, 201, 201, 201, 132, 60, 60, 60, 60, 13, 6, 6, 4, 4, 60, 60, 186, 186, 186, 186, 186, 186, 186, 186] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 669 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113618 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113618/1 /scratch/stefan/7770410/working/building/REAL300020113618 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 846) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/846 `/scratch/stefan/7770410/working/3D/846' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCC1) `REAL300020113618.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113618/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113618 none COCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 16, 11, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 32, 45, 49, 49, 49, 49, 10, 10, 1, 11, 11, 11, 11, 26, 26, 26, 16, 16, 6, 1, 1, 1, 1, 10, 32, 32, 45, 45, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 272 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113618 none COCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 75, 69, 39, 39, 39, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 10, 69, 69, 69, 69, 87, 87, 87, 75, 75, 39, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 69, 69, 69, 69, 69, 69, 69, 69] 201 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 311 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113618 none COCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 3, 3, 3, 11, 11, 11, 69, 69, 69, 154, 201, 201, 201, 201, 201, 69, 69, 11, 1, 1, 1, 1, 9, 9, 9, 5, 5, 3, 11, 11, 11, 11, 69, 154, 154, 201, 201, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 44, 45, 46, 47, 48, 49, 50, 51, 23, 24, 25, 26] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 810 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113618 none COCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 186, 132, 132, 132, 61, 61, 61, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 61, 186, 186, 186, 186, 201, 201, 201, 201, 201, 132, 61, 61, 61, 61, 12, 6, 6, 4, 4, 61, 61, 186, 186, 186, 186, 186, 186, 186, 186] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 675 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113618 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113618 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113618/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113618/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113618 Building REAL300020113619 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113619' /scratch/stefan/7770410/working/building/REAL300020113619 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113619 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113619/0 /scratch/stefan/7770410/working/building/REAL300020113619 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/847 `/scratch/stefan/7770410/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCCC1) `REAL300020113619.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113619 none COCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 36, 11, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 23, 30, 30, 30, 30, 30, 13, 13, 1, 11, 11, 11, 11, 11, 49, 49, 49, 36, 36, 6, 1, 1, 1, 1, 13, 23, 23, 30, 30, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 43, 44, 22] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 266 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113619 none COCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [176, 169, 95, 57, 57, 57, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 13, 95, 95, 95, 95, 95, 176, 176, 176, 169, 169, 57, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95] 201 rigid atoms, others: [38, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 704 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113619 none COCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 2, 2, 2, 11, 11, 11, 95, 95, 95, 112, 135, 135, 135, 135, 135, 95, 95, 11, 1, 1, 1, 1, 1, 11, 11, 11, 5, 5, 2, 11, 11, 11, 11, 95, 112, 112, 135, 135, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 23, 24, 25, 26, 27] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 382 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113619 none COCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 147, 95, 95, 95, 37, 37, 37, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 37, 147, 147, 147, 147, 147, 201, 201, 201, 201, 201, 95, 37, 37, 37, 37, 7, 4, 4, 2, 2, 37, 37, 147, 147, 147, 147, 147, 147, 147, 147, 147, 147] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 730 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113619 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113619/1 /scratch/stefan/7770410/working/building/REAL300020113619 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 848) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/848 `/scratch/stefan/7770410/working/3D/848' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCCC1) `REAL300020113619.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113619/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113619 none COCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 36, 11, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 21, 27, 27, 27, 27, 27, 13, 13, 1, 11, 11, 11, 11, 11, 48, 48, 48, 36, 36, 6, 1, 1, 1, 1, 13, 21, 21, 27, 27, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 43, 44, 22] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 253 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113619 none COCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [178, 172, 98, 57, 57, 57, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 13, 98, 98, 98, 98, 98, 178, 178, 178, 172, 172, 57, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98] 201 rigid atoms, others: [38, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 714 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113619 none COCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 2, 2, 2, 11, 11, 11, 98, 98, 98, 113, 134, 134, 134, 134, 134, 98, 98, 11, 1, 1, 1, 1, 1, 10, 10, 10, 5, 5, 2, 11, 11, 11, 11, 98, 113, 113, 134, 134, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 23, 24, 25, 26, 27] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 360 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113619 none COCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 148, 96, 96, 96, 36, 36, 36, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 36, 148, 148, 148, 148, 148, 201, 201, 201, 201, 201, 96, 36, 36, 36, 36, 7, 4, 4, 2, 2, 36, 36, 148, 148, 148, 148, 148, 148, 148, 148, 148, 148] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 726 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113619 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113619 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113619/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113619/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113619 Building REAL300020113620 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113620' /scratch/stefan/7770410/working/building/REAL300020113620 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113620 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113620/0 /scratch/stefan/7770410/working/building/REAL300020113620 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 849) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/849 `/scratch/stefan/7770410/working/3D/849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCOCC1) `REAL300020113620.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113620 none COCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 40, 11, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 18, 20, 20, 20, 20, 20, 13, 13, 1, 11, 11, 11, 11, 11, 52, 52, 52, 40, 40, 6, 1, 1, 1, 1, 13, 18, 18, 20, 20, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 43, 44, 22] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 229 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113620 none COCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 194, 99, 56, 56, 56, 13, 13, 13, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 1, 1, 13, 99, 99, 99, 99, 99, 200, 200, 200, 194, 194, 56, 13, 13, 13, 13, 1, 3, 3, 5, 5, 13, 13, 99, 99, 99, 99, 99, 99, 99, 99] 201 rigid atoms, others: [38, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 798 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113620 none COCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 1, 1, 1, 2, 2, 2, 11, 11, 11, 99, 99, 99, 106, 111, 111, 111, 111, 111, 99, 99, 11, 1, 1, 1, 1, 1, 10, 10, 10, 6, 6, 2, 11, 11, 11, 11, 99, 106, 106, 111, 111, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 45, 46, 47, 48, 49, 50, 51, 52, 23, 24, 25, 26, 27] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113620 none COCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 115, 75, 75, 75, 26, 26, 26, 6, 6, 6, 4, 2, 1, 1, 1, 1, 1, 1, 6, 6, 26, 115, 115, 115, 115, 115, 201, 201, 201, 201, 201, 75, 26, 26, 26, 26, 6, 4, 4, 2, 2, 26, 26, 115, 115, 115, 115, 115, 115, 115, 115] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 783 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113620 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113620/1 /scratch/stefan/7770410/working/building/REAL300020113620 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 850) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/850 `/scratch/stefan/7770410/working/3D/850' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCOCC1) `REAL300020113620.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113620 none COCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 40, 11, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 18, 20, 20, 20, 20, 20, 13, 13, 1, 11, 11, 11, 11, 11, 52, 52, 52, 40, 40, 6, 1, 1, 1, 1, 13, 18, 18, 20, 20, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 43, 44, 22] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 229 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113620 none COCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 195, 100, 56, 56, 56, 13, 13, 13, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 1, 1, 13, 100, 100, 100, 100, 100, 201, 201, 201, 195, 195, 56, 13, 13, 13, 13, 1, 3, 3, 5, 5, 13, 13, 100, 100, 100, 100, 100, 100, 100, 100] 201 rigid atoms, others: [38, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 802 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113620 none COCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 1, 1, 1, 2, 2, 2, 11, 11, 11, 100, 100, 100, 107, 111, 111, 111, 111, 111, 100, 100, 11, 1, 1, 1, 1, 1, 10, 10, 10, 6, 6, 2, 11, 11, 11, 11, 100, 107, 107, 111, 111, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 45, 46, 47, 48, 49, 50, 51, 52, 23, 24, 25, 26, 27] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113620 none COCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 112, 72, 72, 72, 26, 26, 26, 6, 6, 6, 4, 2, 1, 1, 1, 1, 1, 1, 6, 6, 26, 112, 112, 112, 112, 112, 201, 201, 201, 201, 201, 72, 26, 26, 26, 26, 6, 4, 4, 2, 2, 26, 26, 112, 112, 112, 112, 112, 112, 112, 112] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 793 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113620 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113620 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113620/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113620/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113620 Building REAL300020113621 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113621' /scratch/stefan/7770410/working/building/REAL300020113621 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113621 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113621/0 /scratch/stefan/7770410/working/building/REAL300020113621 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/851 `/scratch/stefan/7770410/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCC1CCOCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113621.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113621 none O=C(CCCC1CCOCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 20, 21, 25, 42, 42, 42, 42, 42, 1, 1, 1, 1, 1, 7, 7, 7, 16, 25, 25, 25, 25, 25, 7, 7, 1, 20, 20, 25, 25, 25, 25, 42, 42, 42, 42, 42, 42, 42, 42, 42, 4, 1, 1, 1, 1, 7, 16, 16, 25, 25, 1, 1] 201 rigid atoms, others: [47, 15, 12, 11, 44, 13, 14, 45, 46, 54, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50, 51, 52]) total number of confs: 289 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113621 none O=C(CCCC1CCOCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 71, 78, 84, 141, 141, 141, 141, 141, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 71, 71, 84, 84, 84, 84, 141, 141, 141, 141, 141, 141, 141, 141, 141, 14, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [48, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54]) total number of confs: 613 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113621 none O=C(CCCC1CCOCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 31, 31, 42, 42, 42, 141, 141, 141, 178, 201, 201, 201, 201, 201, 141, 141, 42, 9, 9, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 42, 42, 42, 42, 141, 178, 178, 201, 201, 42, 42] 201 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 39, 40, 41, 36, 38, 42, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 609 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113621 none O=C(CCCC1CCOCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 107, 112, 118, 201, 201, 201, 201, 201, 26, 26, 26, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 26, 107, 107, 118, 118, 118, 118, 201, 201, 201, 201, 201, 201, 201, 201, 201, 30, 26, 26, 26, 26, 7, 4, 4, 2, 2, 26, 26] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 815 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113621 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113621/1 /scratch/stefan/7770410/working/building/REAL300020113621 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 852) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/852 `/scratch/stefan/7770410/working/3D/852' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCC1CCOCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113621.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113621/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113621 none O=C(CCCC1CCOCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 20, 22, 26, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 7, 7, 7, 16, 25, 25, 25, 25, 25, 7, 7, 1, 20, 20, 26, 26, 26, 26, 43, 43, 43, 43, 43, 43, 43, 43, 43, 4, 1, 1, 1, 1, 7, 16, 16, 25, 25, 1, 1] 201 rigid atoms, others: [47, 15, 12, 11, 44, 13, 14, 45, 46, 54, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50, 51, 52]) total number of confs: 295 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113621 none O=C(CCCC1CCOCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 72, 80, 86, 141, 141, 141, 141, 141, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 72, 72, 86, 86, 86, 86, 141, 141, 141, 141, 141, 141, 141, 141, 141, 14, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [48, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54]) total number of confs: 614 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113621 none O=C(CCCC1CCOCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 32, 32, 43, 43, 43, 141, 141, 141, 179, 201, 201, 201, 201, 201, 141, 141, 43, 9, 9, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 43, 43, 43, 43, 141, 179, 179, 201, 201, 43, 43] 201 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 39, 40, 41, 36, 38, 42, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 612 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113621 none O=C(CCCC1CCOCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 106, 112, 118, 201, 201, 201, 201, 201, 26, 26, 26, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 26, 106, 106, 118, 118, 118, 118, 201, 201, 201, 201, 201, 201, 201, 201, 201, 30, 26, 26, 26, 26, 7, 4, 4, 2, 2, 26, 26] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 815 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113621 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113621 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113621/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113621/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113621 Building REAL300020113622 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113622' /scratch/stefan/7770410/working/building/REAL300020113622 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113622 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113622/0 /scratch/stefan/7770410/working/building/REAL300020113622 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/853 `/scratch/stefan/7770410/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC2(CC2C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCO1) `REAL300020113622.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113622 none CC1CC2(CC2C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 42, 58, 69, 69, 69, 69, 11, 11, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 11, 42, 42, 58, 58, 1, 1, 18, 18, 18, 18] 201 rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 47, 48, 40, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50, 51, 52]) total number of confs: 293 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113622 none CC1CC2(CC2C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 93, 93, 42, 42, 42, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 1, 1, 11, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 42, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 93, 93, 93, 93] 201 rigid atoms, others: [42, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 310 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113622 none CC1CC2(CC2C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 93, 93, 93, 165, 201, 201, 201, 201, 201, 93, 93, 18, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 18, 18, 18, 18, 93, 165, 165, 201, 201, 18, 18, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 36, 34, 49, 50, 35, 52, 51, 25, 26, 27, 5, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 727 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113622 none CC1CC2(CC2C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 151, 151, 151, 70, 70, 70, 14, 14, 14, 7, 4, 1, 1, 1, 1, 1, 1, 14, 14, 70, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 151, 70, 70, 70, 70, 14, 7, 7, 4, 4, 70, 70, 201, 201, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 617 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113622 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113622/1 /scratch/stefan/7770410/working/building/REAL300020113622 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 854) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/854 `/scratch/stefan/7770410/working/3D/854' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC2(CC2C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCO1) `REAL300020113622.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113622 none CC1CC2(CC2C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 42, 58, 69, 69, 69, 69, 11, 11, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 11, 42, 42, 58, 58, 1, 1, 18, 18, 18, 18] 201 rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 47, 48, 40, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50, 51, 52]) total number of confs: 293 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113622 none CC1CC2(CC2C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 94, 94, 42, 42, 42, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 1, 1, 11, 94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 42, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 94, 94, 94, 94] 201 rigid atoms, others: [42, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 314 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113622 none CC1CC2(CC2C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 94, 94, 94, 165, 201, 201, 201, 201, 201, 94, 94, 18, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 18, 18, 18, 18, 94, 165, 165, 201, 201, 18, 18, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 36, 34, 49, 50, 35, 52, 51, 25, 26, 27, 5, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 722 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113622 none CC1CC2(CC2C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 151, 151, 151, 70, 70, 70, 14, 14, 14, 7, 4, 1, 1, 1, 1, 1, 1, 14, 14, 70, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 151, 70, 70, 70, 70, 14, 7, 7, 4, 4, 70, 70, 201, 201, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 617 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113622 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113622 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113622/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113622/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113622 Building REAL300020113623 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113623' /scratch/stefan/7770410/working/building/REAL300020113623 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113623 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113623/0 /scratch/stefan/7770410/working/building/REAL300020113623 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/855 `/scratch/stefan/7770410/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(C2CCC2)C=C1) `REAL300020113623.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113623 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(C2CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 11, 27, 44, 44, 27, 44, 100, 100, 100, 44, 44, 27, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 44, 44, 100, 100, 100, 100, 100, 100, 100, 44, 44] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 404 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113623 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(C2CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 4, 10, 10, 20, 20, 20, 100, 100, 100, 173, 201, 201, 201, 201, 201, 100, 100, 20, 2, 7, 7, 1, 1, 1, 1, 1, 7, 7, 10, 20, 20, 20, 20, 100, 173, 173, 201, 201, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7] 201 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 50, 51]) total number of confs: 717 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113623 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(C2CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 46, 46, 46, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 46, 81, 123, 123, 81, 123, 201, 201, 201, 123, 123, 81, 46, 46, 46, 46, 8, 4, 4, 2, 2, 46, 46, 123, 123, 201, 201, 201, 201, 201, 201, 201, 123, 123] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 831 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113623 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(C2CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 32, 46, 46, 46, 46, 46, 11, 11, 1, 5, 7, 7, 5, 7, 20, 20, 20, 7, 7, 5, 1, 1, 1, 1, 11, 32, 32, 46, 46, 1, 1, 7, 7, 20, 20, 20, 20, 20, 20, 20, 7, 7] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113623 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(C2CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 7, 7, 7, 44, 44, 44, 95, 122, 122, 122, 122, 122, 44, 44, 7, 1, 1, 1, 1, 1, 7, 7, 7, 1, 1, 3, 7, 7, 7, 7, 44, 95, 95, 122, 122, 7, 7, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1] 201 rigid atoms, others: [1, 51, 41, 42, 50, 19, 20, 21, 22, 23, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 481 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113623 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113623/1 /scratch/stefan/7770410/working/building/REAL300020113623 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 856) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/856 `/scratch/stefan/7770410/working/3D/856' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(C2CCC2)C=C1) `REAL300020113623.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113623 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(C2CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 11, 27, 44, 44, 27, 44, 100, 100, 100, 44, 44, 27, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 44, 44, 100, 100, 100, 100, 100, 100, 100, 44, 44] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 404 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113623 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(C2CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 4, 10, 10, 20, 20, 20, 100, 100, 100, 173, 201, 201, 201, 201, 201, 100, 100, 20, 2, 7, 7, 1, 1, 1, 1, 1, 7, 7, 10, 20, 20, 20, 20, 100, 173, 173, 201, 201, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7] 201 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 50, 51]) total number of confs: 717 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113623 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(C2CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 47, 47, 47, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 47, 81, 123, 123, 81, 123, 201, 201, 201, 123, 123, 81, 47, 47, 47, 47, 9, 4, 4, 2, 2, 47, 47, 123, 123, 201, 201, 201, 201, 201, 201, 201, 123, 123] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 829 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113623 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(C2CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 32, 46, 46, 46, 46, 46, 11, 11, 1, 5, 7, 7, 5, 7, 20, 20, 20, 7, 7, 5, 1, 1, 1, 1, 11, 32, 32, 46, 46, 1, 1, 7, 7, 20, 20, 20, 20, 20, 20, 20, 7, 7] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113623 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(C2CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 7, 7, 7, 44, 44, 44, 95, 122, 122, 122, 122, 122, 44, 44, 7, 1, 1, 1, 1, 1, 7, 7, 7, 1, 1, 3, 7, 7, 7, 7, 44, 95, 95, 122, 122, 7, 7, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1] 201 rigid atoms, others: [1, 51, 41, 42, 50, 19, 20, 21, 22, 23, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 481 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113623 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113623 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113623/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113623/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113623 Building REAL300020113624 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113624' /scratch/stefan/7770410/working/building/REAL300020113624 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113624 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113624/0 /scratch/stefan/7770410/working/building/REAL300020113624 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 857) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/857 `/scratch/stefan/7770410/working/3D/857' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1C1CC1) `REAL300020113624.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113624 none CN1N=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 39, 57, 64, 64, 64, 64, 11, 11, 1, 8, 8, 8, 21, 21, 8, 8, 8, 6, 1, 1, 1, 1, 11, 39, 39, 57, 57, 1, 1, 8, 21, 21, 21, 21, 21] 201 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48]) total number of confs: 304 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113624 none CN1N=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 9, 9, 9, 21, 21, 21, 103, 103, 103, 179, 201, 201, 201, 201, 201, 103, 103, 21, 5, 1, 1, 1, 1, 5, 5, 5, 9, 21, 21, 21, 21, 103, 179, 179, 201, 201, 21, 21, 5, 1, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 48, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 672 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113624 none CN1N=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 46, 46, 46, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 48, 48, 48, 103, 103, 48, 48, 48, 46, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 48, 103, 103, 103, 103, 103] 201 rigid atoms, others: [36, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 345 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113624 none CN1N=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 48, 48, 48, 104, 123, 126, 126, 126, 126, 48, 48, 8, 1, 1, 1, 5, 5, 2, 2, 2, 3, 8, 8, 8, 8, 48, 104, 104, 123, 123, 8, 8, 1, 5, 5, 5, 5, 5] 201 rigid atoms, others: [0, 1, 2, 3, 4, 43, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 467 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113624 none CN1N=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [126, 126, 126, 126, 126, 126, 63, 63, 63, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 63, 126, 126, 126, 201, 201, 126, 126, 126, 126, 63, 63, 63, 63, 10, 6, 6, 4, 4, 63, 63, 126, 201, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 663 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113624 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113624/1 /scratch/stefan/7770410/working/building/REAL300020113624 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 858) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/858 `/scratch/stefan/7770410/working/3D/858' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1C1CC1) `REAL300020113624.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113624 none CN1N=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 38, 56, 64, 64, 64, 64, 11, 11, 1, 8, 8, 8, 21, 21, 8, 8, 8, 6, 1, 1, 1, 1, 11, 38, 38, 56, 56, 1, 1, 8, 21, 21, 21, 21, 21] 201 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48]) total number of confs: 303 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113624 none CN1N=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 9, 9, 9, 21, 21, 21, 102, 102, 102, 179, 201, 201, 201, 201, 201, 102, 102, 21, 5, 1, 1, 1, 1, 5, 5, 5, 9, 21, 21, 21, 21, 102, 179, 179, 201, 201, 21, 21, 5, 1, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 48, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 677 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113624 none CN1N=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 46, 46, 46, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 48, 48, 48, 102, 102, 48, 48, 48, 46, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 48, 102, 102, 102, 102, 102] 201 rigid atoms, others: [36, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 343 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113624 none CN1N=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 48, 48, 48, 104, 123, 126, 126, 126, 126, 48, 48, 8, 1, 1, 1, 5, 5, 2, 2, 2, 3, 8, 8, 8, 8, 48, 104, 104, 123, 123, 8, 8, 1, 5, 5, 5, 5, 5] 201 rigid atoms, others: [0, 1, 2, 3, 4, 43, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 467 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113624 none CN1N=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [126, 126, 126, 126, 126, 126, 63, 63, 63, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 63, 126, 126, 126, 201, 201, 126, 126, 126, 126, 63, 63, 63, 63, 11, 6, 6, 4, 4, 63, 63, 126, 201, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 663 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113624 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113624 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113624/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113624/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113624 Building REAL300020113625 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113625' /scratch/stefan/7770410/working/building/REAL300020113625 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113625 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113625/0 /scratch/stefan/7770410/working/building/REAL300020113625 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/859 `/scratch/stefan/7770410/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113625.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113625 none CC(C)C1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 21, 10, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 48, 55, 55, 55, 55, 11, 11, 1, 21, 21, 21, 21, 21, 21, 21, 21, 6, 21, 21, 6, 1, 1, 1, 1, 11, 33, 33, 48, 48, 1, 1] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 266 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113625 none CC(C)C1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 101, 101, 52, 101, 101, 34, 34, 34, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 101, 101, 101, 101, 101, 101, 101, 101, 34, 101, 101, 34, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 322 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113625 none CC(C)C1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 21, 21, 101, 101, 101, 173, 201, 201, 201, 201, 201, 101, 101, 21, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 7, 21, 21, 21, 21, 101, 173, 173, 201, 201, 21, 21] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 35, 36, 38, 37] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 712 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113625 none CC(C)C1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 178, 201, 201, 116, 116, 116, 55, 55, 55, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 55, 201, 201, 201, 201, 201, 201, 201, 201, 116, 201, 201, 116, 55, 55, 55, 55, 10, 6, 6, 4, 4, 55, 55] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 603 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113625 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113625/1 /scratch/stefan/7770410/working/building/REAL300020113625 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 860) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/860 `/scratch/stefan/7770410/working/3D/860' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113625.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113625 none CC(C)C1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 21, 10, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 48, 55, 55, 55, 55, 11, 11, 1, 21, 21, 21, 21, 21, 21, 21, 21, 6, 21, 21, 6, 1, 1, 1, 1, 11, 33, 33, 48, 48, 1, 1] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 266 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113625 none CC(C)C1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 101, 101, 57, 101, 101, 34, 34, 34, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 101, 101, 101, 101, 101, 101, 101, 101, 34, 101, 101, 34, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 332 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113625 none CC(C)C1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 21, 21, 101, 101, 101, 173, 201, 201, 201, 201, 201, 101, 101, 21, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 7, 21, 21, 21, 21, 101, 173, 173, 201, 201, 21, 21] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 35, 36, 38, 37] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 712 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113625 none CC(C)C1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 176, 201, 201, 118, 118, 118, 56, 56, 56, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 56, 201, 201, 201, 201, 201, 201, 201, 201, 118, 201, 201, 118, 56, 56, 56, 56, 12, 6, 6, 4, 4, 56, 56] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 596 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113625 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113625 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113625/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113625/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113625 Building REAL300020113626 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113626' /scratch/stefan/7770410/working/building/REAL300020113626 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113626 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113626/0 /scratch/stefan/7770410/working/building/REAL300020113626 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/861 `/scratch/stefan/7770410/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113626.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113626 none CCN(CC)C(=O)CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 82, 77, 82, 85, 74, 77, 74, 34, 34, 34, 9, 9, 9, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 9, 94, 94, 94, 94, 94, 85, 85, 85, 85, 85, 74, 74, 74, 74, 34, 9, 9, 9, 9, 1, 8, 8, 10, 10, 9, 9] 201 rigid atoms, others: [14, 47, 16, 17, 18, 25, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 448 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113626 none CCN(CC)C(=O)CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 178, 171, 178, 186, 169, 171, 169, 121, 121, 121, 56, 56, 56, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 56, 201, 201, 201, 201, 201, 186, 186, 186, 186, 186, 169, 169, 169, 169, 121, 56, 56, 56, 56, 13, 6, 6, 4, 4, 56, 56] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 814 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113626 none CCN(CC)C(=O)CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 24, 22, 24, 27, 20, 22, 20, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 35, 48, 55, 55, 55, 55, 9, 9, 1, 31, 31, 31, 31, 31, 27, 27, 27, 27, 27, 20, 20, 20, 20, 6, 1, 1, 1, 1, 9, 35, 35, 48, 48, 1, 1] 201 rigid atoms, others: [11, 15, 44, 43, 12, 13, 14, 45, 52, 46, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 349 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113626 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113626/1 /scratch/stefan/7770410/working/building/REAL300020113626 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 862) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/862 `/scratch/stefan/7770410/working/3D/862' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113626.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113626 none CCN(CC)C(=O)CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 80, 75, 80, 83, 72, 75, 72, 33, 33, 33, 9, 9, 9, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 9, 92, 92, 92, 92, 92, 83, 83, 83, 83, 83, 72, 72, 72, 72, 33, 9, 9, 9, 9, 1, 8, 8, 10, 10, 9, 9] 201 rigid atoms, others: [14, 47, 16, 17, 18, 25, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 440 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113626 none CCN(CC)C(=O)CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 179, 172, 179, 187, 170, 172, 170, 122, 122, 122, 56, 56, 56, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 56, 201, 201, 201, 201, 201, 187, 187, 187, 187, 187, 170, 170, 170, 170, 122, 56, 56, 56, 56, 12, 6, 6, 4, 4, 56, 56] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 809 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113626 none CCN(CC)C(=O)CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 24, 22, 24, 27, 20, 22, 20, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 35, 48, 56, 56, 56, 56, 9, 9, 1, 31, 31, 31, 31, 31, 27, 27, 27, 27, 27, 20, 20, 20, 20, 6, 1, 1, 1, 1, 9, 35, 35, 48, 48, 1, 1] 201 rigid atoms, others: [11, 15, 44, 43, 12, 13, 14, 45, 52, 46, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 351 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113626 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113626 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113626/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113626/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113626 Building REAL300020113627 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113627' /scratch/stefan/7770410/working/building/REAL300020113627 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113627 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113627/0 /scratch/stefan/7770410/working/building/REAL300020113627 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 863) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/863 `/scratch/stefan/7770410/working/3D/863' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1) `REAL300020113627.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113627 none C=CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 99, 38, 38, 38, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 99, 106, 106, 99, 106, 106, 111, 111, 111, 99, 38, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 106, 106, 106, 106, 106] 201 rigid atoms, others: [37, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 477 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113627 none C=CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 96, 96, 96, 48, 48, 48, 11, 11, 11, 4, 4, 1, 1, 1, 1, 1, 1, 11, 11, 48, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 96, 48, 48, 48, 48, 11, 4, 4, 4, 4, 48, 48, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 695 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113627 none C=CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 20, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 34, 48, 52, 52, 52, 52, 11, 11, 1, 20, 26, 26, 20, 26, 26, 30, 30, 30, 20, 6, 1, 1, 1, 1, 11, 34, 34, 48, 48, 1, 1, 26, 26, 26, 26, 26] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 42, 43, 21] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48]) total number of confs: 339 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113627 none C=CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 1, 4, 11, 11, 11, 26, 26, 26, 106, 106, 106, 168, 201, 201, 201, 201, 201, 106, 106, 26, 1, 1, 1, 1, 1, 1, 6, 6, 6, 4, 11, 26, 26, 26, 26, 106, 168, 168, 201, 201, 26, 26, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 44, 45, 46, 47, 48, 22, 23, 24, 25, 26, 27] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 702 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113627 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113627/1 /scratch/stefan/7770410/working/building/REAL300020113627 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 864) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/864 `/scratch/stefan/7770410/working/3D/864' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1) `REAL300020113627.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113627/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113627 none C=CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 100, 38, 38, 38, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 100, 107, 107, 100, 107, 107, 112, 112, 112, 100, 38, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 107, 107, 107, 107, 107] 201 rigid atoms, others: [37, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 480 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113627 none C=CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 95, 95, 95, 47, 47, 47, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 10, 10, 47, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 95, 47, 47, 47, 47, 10, 4, 4, 4, 4, 47, 47, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 697 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113627 none C=CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 20, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 34, 48, 52, 52, 52, 52, 11, 11, 1, 20, 26, 26, 20, 26, 26, 30, 30, 30, 20, 6, 1, 1, 1, 1, 11, 34, 34, 48, 48, 1, 1, 26, 26, 26, 26, 26] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 42, 43, 21] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48]) total number of confs: 339 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113627 none C=CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 1, 4, 11, 11, 11, 26, 26, 26, 107, 107, 107, 167, 201, 201, 201, 201, 201, 107, 107, 26, 1, 1, 1, 1, 1, 1, 6, 6, 6, 4, 11, 26, 26, 26, 26, 107, 167, 167, 201, 201, 26, 26, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 44, 45, 46, 47, 48, 22, 23, 24, 25, 26, 27] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 697 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113627 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113627 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113627/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113627/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113627 Building REAL300020113628 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113628' /scratch/stefan/7770410/working/building/REAL300020113628 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113628 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113628/0 /scratch/stefan/7770410/working/building/REAL300020113628 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/865 `/scratch/stefan/7770410/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCCC1) `REAL300020113628.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113628 none C=CCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 26, 11, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 21, 26, 26, 26, 26, 26, 13, 13, 1, 11, 11, 11, 11, 11, 35, 35, 35, 26, 26, 6, 1, 1, 1, 1, 13, 21, 21, 26, 26, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 43, 44, 22] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 229 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113628 none C=CCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 163, 99, 53, 53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 13, 99, 99, 99, 99, 99, 165, 165, 165, 163, 163, 53, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99] 201 rigid atoms, others: [38, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 731 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113628 none C=CCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 1, 1, 1, 2, 2, 2, 11, 11, 11, 99, 99, 99, 119, 137, 137, 137, 137, 137, 99, 99, 11, 1, 1, 1, 1, 1, 10, 10, 10, 6, 6, 2, 11, 11, 11, 11, 99, 119, 119, 137, 137, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 23, 24, 25, 26, 27] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 376 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113628 none C=CCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 145, 79, 79, 79, 28, 28, 28, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 28, 145, 145, 145, 145, 145, 201, 201, 201, 201, 201, 79, 28, 28, 28, 28, 7, 4, 4, 2, 2, 28, 28, 145, 145, 145, 145, 145, 145, 145, 145, 145, 145] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 819 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113628 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113628/1 /scratch/stefan/7770410/working/building/REAL300020113628 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 866) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/866 `/scratch/stefan/7770410/working/3D/866' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCCC1) `REAL300020113628.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113628/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113628 none C=CCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 26, 11, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 21, 26, 26, 26, 26, 26, 13, 13, 1, 11, 11, 11, 11, 11, 36, 36, 36, 26, 26, 6, 1, 1, 1, 1, 13, 21, 21, 26, 26, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 43, 44, 22] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 233 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113628 none C=CCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [166, 164, 99, 53, 53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 13, 99, 99, 99, 99, 99, 166, 166, 166, 164, 164, 53, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99] 201 rigid atoms, others: [38, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 737 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113628 none C=CCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 1, 1, 1, 2, 2, 2, 11, 11, 11, 99, 99, 99, 118, 136, 136, 136, 136, 136, 99, 99, 11, 1, 1, 1, 1, 1, 10, 10, 10, 6, 6, 2, 11, 11, 11, 11, 99, 118, 118, 136, 136, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 23, 24, 25, 26, 27] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 373 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113628 none C=CCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 144, 79, 79, 79, 28, 28, 28, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 28, 144, 144, 144, 144, 144, 201, 201, 201, 201, 201, 79, 28, 28, 28, 28, 7, 4, 4, 2, 2, 28, 28, 144, 144, 144, 144, 144, 144, 144, 144, 144, 144] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 818 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113628 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113628 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113628/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113628/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113628 Building REAL300020113629 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113629' /scratch/stefan/7770410/working/building/REAL300020113629 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113629 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113629/0 /scratch/stefan/7770410/working/building/REAL300020113629 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/867 `/scratch/stefan/7770410/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1C(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113629.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113629 none CC1=CC=CC=C1C(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 15, 23, 23, 15, 6, 15, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 45, 61, 71, 71, 71, 71, 11, 11, 1, 23, 23, 23, 23, 15, 23, 23, 15, 15, 15, 15, 6, 1, 1, 1, 1, 11, 45, 45, 61, 61, 1, 1] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 351 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113629 none CC1=CC=CC=C1C(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 86, 112, 112, 86, 40, 86, 40, 40, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 11, 112, 112, 112, 112, 86, 112, 112, 86, 86, 86, 86, 40, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 483 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113629 none CC1=CC=CC=C1C(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 23, 23, 23, 112, 112, 112, 183, 201, 201, 201, 201, 201, 112, 112, 23, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 4, 8, 23, 23, 23, 23, 112, 183, 183, 201, 201, 23, 23] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 33, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 673 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113629 none CC1=CC=CC=C1C(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 153, 201, 153, 153, 72, 72, 72, 15, 15, 15, 7, 4, 1, 1, 1, 1, 1, 1, 15, 15, 72, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 153, 72, 72, 72, 72, 15, 7, 7, 4, 4, 72, 72] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 677 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113629 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113629/1 /scratch/stefan/7770410/working/building/REAL300020113629 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 868) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/868 `/scratch/stefan/7770410/working/3D/868' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1C(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113629.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113629/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113629 none CC1=CC=CC=C1C(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 15, 23, 23, 15, 6, 15, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 45, 61, 71, 71, 71, 71, 11, 11, 1, 23, 23, 23, 23, 15, 23, 23, 15, 15, 15, 15, 6, 1, 1, 1, 1, 11, 45, 45, 61, 61, 1, 1] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 351 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113629 none CC1=CC=CC=C1C(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 86, 112, 112, 86, 40, 86, 40, 40, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 11, 112, 112, 112, 112, 86, 112, 112, 86, 86, 86, 86, 40, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 483 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113629 none CC1=CC=CC=C1C(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 23, 23, 23, 112, 112, 112, 183, 201, 201, 201, 201, 201, 112, 112, 23, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 4, 8, 23, 23, 23, 23, 112, 183, 183, 201, 201, 23, 23] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 33, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 673 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113629 none CC1=CC=CC=C1C(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 154, 201, 154, 154, 73, 73, 73, 16, 16, 16, 7, 4, 1, 1, 1, 1, 1, 1, 16, 16, 73, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 154, 73, 73, 73, 73, 16, 7, 7, 4, 4, 73, 73] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 675 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113629 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113629 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113629/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113629/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113629 Building REAL300020113630 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113630' /scratch/stefan/7770410/working/building/REAL300020113630 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113630 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113630/0 /scratch/stefan/7770410/working/building/REAL300020113630 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/869 `/scratch/stefan/7770410/working/3D/869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(F)CC1=CC=CC=C1) `REAL300020113630.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113630 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(F)CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 15, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 32, 68, 68, 106, 106, 106, 106, 106, 106, 32, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9, 68, 106, 106, 106, 106, 106, 106, 106] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 472 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113630 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(F)CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 15, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [129, 129, 55, 55, 55, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 55, 129, 170, 170, 201, 201, 201, 201, 201, 201, 129, 55, 55, 55, 55, 13, 6, 6, 4, 4, 55, 55, 170, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 762 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113630 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(F)CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 15, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 30, 45, 53, 53, 53, 53, 9, 9, 1, 6, 18, 18, 32, 32, 32, 32, 32, 32, 6, 1, 1, 1, 1, 9, 30, 30, 45, 45, 1, 1, 18, 32, 32, 32, 32, 32, 32, 32] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 329 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113630 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(F)CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 15, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 15, 15, 32, 32, 32, 106, 106, 106, 167, 201, 201, 201, 201, 201, 106, 106, 32, 1, 5, 1, 1, 1, 1, 1, 1, 1, 15, 32, 32, 32, 32, 106, 167, 167, 201, 201, 32, 32, 5, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 19, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 726 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113630 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113630/1 /scratch/stefan/7770410/working/building/REAL300020113630 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 870) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/870 `/scratch/stefan/7770410/working/3D/870' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(F)CC1=CC=CC=C1) `REAL300020113630.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113630 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(F)CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 15, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 32, 68, 68, 105, 105, 105, 105, 105, 105, 32, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9, 68, 105, 105, 105, 105, 105, 105, 105] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 466 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113630 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(F)CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 15, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 54, 54, 54, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 54, 128, 170, 170, 201, 201, 201, 201, 201, 201, 128, 54, 54, 54, 54, 12, 6, 6, 4, 4, 54, 54, 170, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 767 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113630 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(F)CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 15, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 29, 44, 53, 53, 53, 53, 9, 9, 1, 6, 18, 18, 32, 32, 32, 32, 32, 32, 6, 1, 1, 1, 1, 9, 29, 29, 44, 44, 1, 1, 18, 32, 32, 32, 32, 32, 32, 32] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 328 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113630 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(F)CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 15, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 15, 15, 32, 32, 32, 105, 105, 105, 166, 201, 201, 201, 201, 201, 105, 105, 32, 1, 5, 1, 1, 1, 1, 1, 1, 1, 15, 32, 32, 32, 32, 105, 166, 166, 201, 201, 32, 32, 5, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 19, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 730 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113630 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113630 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113630/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113630/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113630 Building REAL300020113631 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113631' /scratch/stefan/7770410/working/building/REAL300020113631 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113631 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113631/0 /scratch/stefan/7770410/working/building/REAL300020113631 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/871 `/scratch/stefan/7770410/working/3D/871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCCC1) `REAL300020113631.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113631 none CCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 11, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 36, 44, 44, 44, 44, 44, 13, 13, 1, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 13, 36, 36, 44, 44, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 42, 43, 21] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 208 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113631 none CCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 59, 59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 111, 111, 111, 111, 111, 111, 111, 111, 111, 111, 59, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 111, 111, 111, 111, 111, 111, 111, 111, 111, 111] 201 rigid atoms, others: [37, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 381 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113631 none CCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 3, 3, 3, 11, 11, 11, 111, 111, 111, 176, 201, 201, 201, 201, 201, 111, 111, 11, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 3, 11, 11, 11, 11, 111, 176, 176, 201, 201, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 22, 23, 24, 25, 26] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 635 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113631 none CCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 112, 112, 112, 49, 49, 49, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 49, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 112, 49, 49, 49, 49, 8, 4, 4, 2, 2, 49, 49, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 653 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113631 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113631/1 /scratch/stefan/7770410/working/building/REAL300020113631 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 872) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/872 `/scratch/stefan/7770410/working/3D/872' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCCC1) `REAL300020113631.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113631/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113631 none CCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 11, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 36, 44, 44, 44, 44, 44, 13, 13, 1, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 13, 36, 36, 44, 44, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 42, 43, 21] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 208 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113631 none CCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 59, 59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 111, 111, 111, 111, 111, 111, 111, 111, 111, 111, 59, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 111, 111, 111, 111, 111, 111, 111, 111, 111, 111] 201 rigid atoms, others: [37, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 381 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113631 none CCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 3, 3, 3, 11, 11, 11, 111, 111, 111, 176, 201, 201, 201, 201, 201, 111, 111, 11, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 3, 11, 11, 11, 11, 111, 176, 176, 201, 201, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 22, 23, 24, 25, 26] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 635 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113631 none CCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 112, 112, 112, 49, 49, 49, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 49, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 112, 49, 49, 49, 49, 8, 4, 4, 2, 2, 49, 49, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 653 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113631 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113631 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113631/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113631/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113631 Building REAL300020113632 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113632' /scratch/stefan/7770410/working/building/REAL300020113632 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113632 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113632/0 /scratch/stefan/7770410/working/building/REAL300020113632 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 873) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/873 `/scratch/stefan/7770410/working/3D/873' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)C1=CC=CC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113632.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113632 none O=C(CNC(=O)C1=CC=CC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 28, 31, 31, 31, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 8, 8, 8, 29, 41, 41, 41, 41, 41, 8, 8, 1, 28, 28, 31, 32, 32, 32, 32, 6, 1, 1, 1, 1, 8, 29, 29, 41, 41, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 46, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 272 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113632 none O=C(CNC(=O)C1=CC=CC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 96, 100, 100, 100, 101, 101, 101, 101, 101, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 96, 96, 100, 101, 101, 101, 101, 26, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 376 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113632 none O=C(CNC(=O)C1=CC=CC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 32, 32, 32, 101, 101, 101, 173, 201, 201, 201, 201, 201, 101, 101, 32, 6, 6, 2, 1, 1, 1, 1, 15, 32, 32, 32, 32, 101, 173, 173, 201, 201, 32, 32] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 712 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113632 none O=C(CNC(=O)C1=CC=CC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 197, 201, 201, 201, 201, 201, 201, 201, 201, 42, 42, 42, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 42, 197, 197, 201, 201, 201, 201, 201, 83, 42, 42, 42, 42, 9, 4, 4, 2, 2, 42, 42] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 738 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113632 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113632/1 /scratch/stefan/7770410/working/building/REAL300020113632 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 874) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/874 `/scratch/stefan/7770410/working/3D/874' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)C1=CC=CC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113632.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113632 none O=C(CNC(=O)C1=CC=CC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 28, 31, 31, 31, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 9, 9, 9, 31, 43, 43, 43, 43, 43, 9, 9, 1, 28, 28, 31, 32, 32, 32, 32, 6, 1, 1, 1, 1, 9, 31, 31, 43, 43, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 46, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 276 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113632 none O=C(CNC(=O)C1=CC=CC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 96, 101, 101, 101, 102, 102, 102, 102, 102, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 9, 96, 96, 101, 102, 102, 102, 102, 27, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 376 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113632 none O=C(CNC(=O)C1=CC=CC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 32, 32, 32, 102, 102, 102, 172, 201, 201, 201, 201, 201, 102, 102, 32, 6, 6, 2, 1, 1, 1, 1, 15, 32, 32, 32, 32, 102, 172, 172, 201, 201, 32, 32] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 707 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113632 none O=C(CNC(=O)C1=CC=CC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 198, 201, 201, 201, 201, 201, 201, 201, 201, 44, 44, 44, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 44, 198, 198, 201, 201, 201, 201, 201, 85, 44, 44, 44, 44, 9, 4, 4, 2, 2, 44, 44] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 730 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113632 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113632 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113632/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113632/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113632 Building REAL300020113633 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113633' /scratch/stefan/7770410/working/building/REAL300020113633 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113633 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113633/0 /scratch/stefan/7770410/working/building/REAL300020113633 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 875) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/875 `/scratch/stefan/7770410/working/3D/875' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=N1) `REAL300020113633.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113633 none CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 28, 42, 44, 44, 44, 44, 11, 11, 1, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 11, 28, 28, 42, 42, 1, 1, 21, 21, 21] 201 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 202 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113633 none CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 92, 33, 33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 92, 92, 92, 92, 92, 92, 92, 92, 33, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 92, 92, 92] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 194 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113633 none CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 9, 21, 21, 21, 92, 92, 92, 151, 201, 201, 201, 201, 201, 92, 92, 21, 1, 1, 1, 2, 2, 2, 1, 1, 9, 21, 21, 21, 21, 92, 151, 151, 201, 201, 21, 21, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 779 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113633 none CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 97, 97, 97, 47, 47, 47, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 47, 201, 201, 201, 201, 201, 201, 201, 201, 97, 47, 47, 47, 47, 11, 6, 6, 4, 4, 47, 47, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 432 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113633 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113633/1 /scratch/stefan/7770410/working/building/REAL300020113633 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 876) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/876 `/scratch/stefan/7770410/working/3D/876' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=N1) `REAL300020113633.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113633 none CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 28, 41, 43, 43, 43, 43, 11, 11, 1, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 11, 28, 28, 41, 41, 1, 1, 21, 21, 21] 201 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 196 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113633 none CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 92, 32, 32, 32, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 92, 92, 92, 92, 92, 92, 92, 92, 32, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 92, 92, 92] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 191 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113633 none CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 9, 21, 21, 21, 92, 92, 92, 151, 201, 201, 201, 201, 201, 92, 92, 21, 1, 1, 1, 2, 2, 2, 1, 1, 9, 21, 21, 21, 21, 92, 151, 151, 201, 201, 21, 21, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 780 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113633 none CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 94, 94, 94, 44, 44, 44, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 44, 201, 201, 201, 201, 201, 201, 201, 201, 94, 44, 44, 44, 44, 10, 6, 6, 4, 4, 44, 44, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 429 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113633 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113633 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113633/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113633/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113633 Building REAL300020113634 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113634' /scratch/stefan/7770410/working/building/REAL300020113634 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113634 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113634/0 /scratch/stefan/7770410/working/building/REAL300020113634 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 877) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/877 `/scratch/stefan/7770410/working/3D/877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=C2CCC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)CN12) `REAL300020113634.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113634 none CC1=NN=C2CCC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 29, 43, 43, 43, 43, 43, 13, 13, 1, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 6, 1, 1, 1, 1, 13, 29, 29, 43, 43, 1, 1, 36, 36] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50]) total number of confs: 258 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113634 none CC1=NN=C2CCC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 148, 148, 148, 148, 148, 60, 60, 60, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 148, 148, 148, 148, 148, 148, 148, 148, 148, 148, 60, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 148, 148] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 451 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113634 none CC1=NN=C2CCC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 36, 36, 36, 148, 148, 148, 182, 201, 201, 201, 201, 201, 148, 148, 36, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 10, 36, 36, 36, 36, 148, 182, 182, 201, 201, 36, 36, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 34, 49, 50, 35, 36, 33, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 535 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113634 none CC1=NN=C2CCC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 134, 134, 134, 44, 44, 44, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 44, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 134, 44, 44, 44, 44, 8, 4, 4, 2, 2, 44, 44, 201, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 595 number of broken/clashed sets: 2 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113634 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113634/1 /scratch/stefan/7770410/working/building/REAL300020113634 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 878) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/878 `/scratch/stefan/7770410/working/3D/878' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=C2CCC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)CN12) `REAL300020113634.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113634 none CC1=NN=C2CCC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 29, 43, 43, 43, 43, 43, 13, 13, 1, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 6, 1, 1, 1, 1, 13, 29, 29, 43, 43, 1, 1, 36, 36] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50]) total number of confs: 258 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113634 none CC1=NN=C2CCC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 148, 148, 148, 148, 148, 60, 60, 60, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 148, 148, 148, 148, 148, 148, 148, 148, 148, 148, 60, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 148, 148] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 451 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113634 none CC1=NN=C2CCC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 36, 36, 36, 148, 148, 148, 181, 201, 201, 201, 201, 201, 148, 148, 36, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 10, 36, 36, 36, 36, 148, 181, 181, 201, 201, 36, 36, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 34, 49, 50, 35, 36, 33, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 535 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113634 none CC1=NN=C2CCC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 134, 134, 134, 43, 43, 43, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 43, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 134, 43, 43, 43, 43, 8, 4, 4, 2, 2, 43, 43, 201, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 595 number of broken/clashed sets: 2 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113634 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113634 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113634/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113634/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113634 Building REAL300020113635 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113635' /scratch/stefan/7770410/working/building/REAL300020113635 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113635 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113635/0 /scratch/stefan/7770410/working/building/REAL300020113635 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/879 `/scratch/stefan/7770410/working/3D/879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113635.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113635 none CN(C)S(=O)(=O)CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 109, 113, 113, 95, 26, 26, 26, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 8, 113, 113, 113, 113, 113, 113, 109, 109, 95, 95, 26, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 479 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113635 none CN(C)S(=O)(=O)CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 192, 93, 93, 93, 43, 43, 43, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 43, 201, 201, 201, 201, 201, 201, 201, 201, 192, 192, 93, 43, 43, 43, 43, 10, 6, 6, 4, 4, 43, 43] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 760 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113635 none CN(C)S(=O)(=O)CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 30, 36, 36, 26, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 27, 40, 42, 42, 42, 42, 8, 8, 1, 36, 36, 36, 36, 36, 36, 30, 30, 26, 26, 6, 1, 1, 1, 1, 8, 27, 27, 40, 40, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113635 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113635/1 /scratch/stefan/7770410/working/building/REAL300020113635 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 880) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/880 `/scratch/stefan/7770410/working/3D/880' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113635.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113635 none CN(C)S(=O)(=O)CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 108, 112, 112, 94, 25, 25, 25, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 8, 112, 112, 112, 112, 112, 112, 108, 108, 94, 94, 25, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 477 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113635 none CN(C)S(=O)(=O)CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 192, 94, 94, 94, 44, 44, 44, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 44, 201, 201, 201, 201, 201, 201, 201, 201, 192, 192, 94, 44, 44, 44, 44, 11, 6, 6, 4, 4, 44, 44] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 759 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113635 none CN(C)S(=O)(=O)CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 30, 36, 36, 26, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 27, 40, 42, 42, 42, 42, 8, 8, 1, 36, 36, 36, 36, 36, 36, 30, 30, 26, 26, 6, 1, 1, 1, 1, 8, 27, 27, 40, 40, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113635 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113635 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113635/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113635/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113635 Building REAL300020113636 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113636' /scratch/stefan/7770410/working/building/REAL300020113636 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113636 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113636/0 /scratch/stefan/7770410/working/building/REAL300020113636 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/881 `/scratch/stefan/7770410/working/3D/881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(F)C=C1) `REAL300020113636.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113636 none CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 89, 28, 28, 28, 9, 9, 9, 1, 1, 1, 1, 1, 5, 7, 8, 8, 8, 8, 1, 1, 9, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 89, 89, 28, 9, 9, 9, 9, 1, 5, 5, 7, 7, 9, 9, 106, 106, 106, 106] 201 rigid atoms, others: [8, 9, 10, 11, 12, 40, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 433 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113636 none CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 185, 76, 76, 76, 40, 40, 40, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 40, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 185, 185, 76, 40, 40, 40, 40, 9, 5, 5, 3, 3, 40, 40, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 792 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113636 none CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 22, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 24, 38, 39, 39, 39, 39, 9, 9, 1, 29, 31, 31, 29, 31, 31, 31, 29, 29, 29, 29, 22, 22, 6, 1, 1, 1, 1, 9, 24, 24, 38, 38, 1, 1, 31, 31, 31, 31] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 39, 45, 46, 21, 38, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113636 none CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 6, 16, 16, 16, 31, 31, 31, 106, 106, 106, 158, 201, 201, 201, 201, 201, 106, 106, 31, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 6, 16, 31, 31, 31, 31, 106, 158, 158, 201, 201, 31, 31, 1, 1, 1, 1] 201 rigid atoms, others: [1, 47, 48, 49, 50, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 738 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113636 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113636/1 /scratch/stefan/7770410/working/building/REAL300020113636 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 882) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/882 `/scratch/stefan/7770410/working/3D/882' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(F)C=C1) `REAL300020113636.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113636/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113636 none CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 88, 27, 27, 27, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 9, 105, 105, 105, 105, 105, 105, 105, 105, 105, 105, 105, 88, 88, 27, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 105, 105, 105, 105] 201 rigid atoms, others: [8, 9, 10, 11, 12, 40, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 434 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113636 none CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 185, 76, 76, 76, 39, 39, 39, 8, 8, 8, 5, 3, 1, 1, 1, 1, 1, 1, 8, 8, 39, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 185, 185, 76, 39, 39, 39, 39, 8, 5, 5, 3, 3, 39, 39, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 790 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113636 none CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 22, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 25, 39, 40, 40, 40, 40, 9, 9, 1, 29, 31, 31, 29, 31, 31, 31, 29, 29, 29, 29, 22, 22, 6, 1, 1, 1, 1, 9, 25, 25, 39, 39, 1, 1, 31, 31, 31, 31] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 39, 45, 46, 21, 38, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50]) total number of confs: 293 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113636 none CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 6, 16, 16, 16, 31, 31, 31, 105, 105, 105, 158, 201, 201, 201, 201, 201, 105, 105, 31, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 6, 16, 31, 31, 31, 31, 105, 158, 158, 201, 201, 31, 31, 1, 1, 1, 1] 201 rigid atoms, others: [1, 47, 48, 49, 50, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 743 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113636 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113636 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113636/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113636/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113636 Building REAL300020113637 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113637' /scratch/stefan/7770410/working/building/REAL300020113637 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113637 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113637/0 /scratch/stefan/7770410/working/building/REAL300020113637 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/883 `/scratch/stefan/7770410/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1) `REAL300020113637.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113637 none CCN(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 96, 70, 20, 20, 20, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 96, 106, 106, 103, 106, 106, 110, 110, 110, 110, 110, 70, 70, 20, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 106, 106, 104, 106, 106] 201 rigid atoms, others: [9, 10, 11, 12, 13, 20, 21, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 489 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113637 none CCN(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [191, 189, 138, 54, 54, 54, 36, 36, 36, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 36, 189, 199, 199, 199, 199, 199, 191, 191, 191, 191, 191, 138, 138, 54, 36, 36, 36, 36, 9, 4, 4, 2, 2, 36, 36, 199, 199, 199, 199, 199] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 746 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113637 none CCN(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 30, 18, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 20, 32, 32, 32, 32, 32, 7, 7, 1, 30, 37, 37, 33, 37, 37, 42, 42, 42, 42, 42, 18, 18, 5, 1, 1, 1, 1, 7, 20, 20, 32, 32, 1, 1, 37, 37, 34, 37, 37] 201 rigid atoms, others: [37, 6, 7, 8, 9, 10, 39, 46, 47, 40, 22, 38] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50, 51, 52]) total number of confs: 339 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113637 none CCN(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 5, 12, 19, 19, 19, 37, 37, 37, 106, 106, 106, 163, 199, 199, 199, 199, 199, 106, 106, 37, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 12, 12, 19, 37, 37, 37, 37, 106, 163, 163, 199, 199, 37, 37, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 48, 49, 50, 51, 52, 23, 24, 25, 26, 27, 28] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 767 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113637 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113637/1 /scratch/stefan/7770410/working/building/REAL300020113637 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 884) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/884 `/scratch/stefan/7770410/working/3D/884' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1) `REAL300020113637.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113637 none CCN(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 95, 70, 20, 20, 20, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 95, 105, 105, 102, 105, 105, 108, 108, 108, 108, 108, 70, 70, 20, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 105, 105, 103, 105, 105] 201 rigid atoms, others: [9, 10, 11, 12, 13, 20, 21, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 479 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113637 none CCN(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [191, 189, 138, 56, 56, 56, 38, 38, 38, 12, 12, 12, 4, 2, 1, 1, 1, 1, 1, 1, 12, 12, 38, 189, 199, 199, 199, 199, 199, 191, 191, 191, 191, 191, 138, 138, 56, 38, 38, 38, 38, 12, 4, 4, 2, 2, 38, 38, 199, 199, 199, 199, 199] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 741 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113637 none CCN(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 30, 18, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 20, 32, 32, 32, 32, 32, 7, 7, 1, 30, 37, 37, 33, 37, 37, 42, 42, 42, 42, 42, 18, 18, 5, 1, 1, 1, 1, 7, 20, 20, 32, 32, 1, 1, 37, 37, 34, 37, 37] 201 rigid atoms, others: [37, 6, 7, 8, 9, 10, 39, 46, 47, 40, 22, 38] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50, 51, 52]) total number of confs: 339 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113637 none CCN(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 5, 12, 19, 19, 19, 37, 37, 37, 105, 105, 105, 163, 199, 199, 199, 199, 199, 105, 105, 37, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 12, 12, 19, 37, 37, 37, 37, 105, 163, 163, 199, 199, 37, 37, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 48, 49, 50, 51, 52, 23, 24, 25, 26, 27, 28] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 771 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113637 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113637 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113637/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113637/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113637 Building REAL300020113638 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113638' /scratch/stefan/7770410/working/building/REAL300020113638 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113638 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113638/0 /scratch/stefan/7770410/working/building/REAL300020113638 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 885) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/885 `/scratch/stefan/7770410/working/3D/885' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC=C1) `REAL300020113638.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113638 none CC(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 33, 48, 57, 57, 57, 57, 11, 11, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 11, 33, 33, 48, 48, 1, 1, 19, 19] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 44, 45, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47]) total number of confs: 235 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113638 none CC(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 95, 31, 31, 31, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 31, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 95, 95] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 204 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113638 none CC(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 7, 7, 7, 19, 19, 19, 95, 95, 95, 151, 201, 201, 201, 201, 201, 95, 95, 19, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 7, 19, 19, 19, 19, 95, 151, 151, 201, 201, 19, 19, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 46, 47, 24, 25, 26] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 750 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113638 none CC(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 120, 120, 120, 57, 57, 57, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 57, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 120, 57, 57, 57, 57, 10, 6, 6, 4, 4, 57, 57, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 484 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113638 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113638/1 /scratch/stefan/7770410/working/building/REAL300020113638 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 886) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/886 `/scratch/stefan/7770410/working/3D/886' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC=C1) `REAL300020113638.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113638/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113638 none CC(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 33, 48, 57, 57, 57, 57, 11, 11, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 11, 33, 33, 48, 48, 1, 1, 19, 19] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 44, 45, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47]) total number of confs: 235 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113638 none CC(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 95, 31, 31, 31, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 31, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 95, 95] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 204 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113638 none CC(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 7, 7, 7, 19, 19, 19, 95, 95, 95, 150, 201, 201, 201, 201, 201, 95, 95, 19, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 7, 19, 19, 19, 19, 95, 150, 150, 201, 201, 19, 19, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 46, 47, 24, 25, 26] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 750 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113638 none CC(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 120, 120, 120, 57, 57, 57, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 57, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 120, 57, 57, 57, 57, 10, 6, 6, 4, 4, 57, 57, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 485 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113638 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113638 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113638/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113638/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113638 Building REAL300020113639 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113639' /scratch/stefan/7770410/working/building/REAL300020113639 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113639 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113639/0 /scratch/stefan/7770410/working/building/REAL300020113639 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 887) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/887 `/scratch/stefan/7770410/working/3D/887' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC=C1) `REAL300020113639.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113639 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [40, 26, 26, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 24, 32, 38, 38, 38, 38, 6, 6, 1, 26, 26, 26, 40, 40, 40, 40, 40, 6, 1, 1, 1, 1, 6, 24, 24, 32, 32, 1, 1, 26, 26] 146 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44]) total number of confs: 254 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113639 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [72, 51, 51, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 8, 11, 14, 14, 14, 14, 1, 1, 6, 51, 51, 51, 72, 72, 72, 72, 72, 20, 6, 6, 6, 6, 1, 8, 8, 11, 11, 6, 6, 51, 51] 146 rigid atoms, others: [36, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 268 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113639 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 8, 8, 8, 26, 26, 26, 51, 51, 51, 87, 102, 104, 104, 104, 104, 51, 51, 26, 1, 1, 1, 5, 5, 5, 5, 5, 8, 26, 26, 26, 26, 51, 87, 87, 102, 102, 26, 26, 1, 1] 146 rigid atoms, others: [1, 2, 3, 4, 43, 44, 23, 24, 25] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 393 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113639 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [148, 106, 106, 69, 69, 69, 40, 40, 40, 17, 17, 17, 8, 4, 1, 1, 1, 1, 1, 1, 17, 17, 40, 106, 106, 106, 148, 148, 148, 148, 148, 69, 40, 40, 40, 40, 17, 8, 8, 4, 4, 40, 40, 106, 106] 148 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 519 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113639 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113639/1 /scratch/stefan/7770410/working/building/REAL300020113639 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 888) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/888 `/scratch/stefan/7770410/working/3D/888' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC=C1) `REAL300020113639.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113639/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113639 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [40, 26, 26, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 22, 30, 35, 35, 35, 35, 6, 6, 1, 26, 26, 26, 40, 40, 40, 40, 40, 6, 1, 1, 1, 1, 6, 22, 22, 30, 30, 1, 1, 26, 26] 142 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44]) total number of confs: 246 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113639 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [69, 48, 48, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 6, 48, 48, 48, 69, 69, 69, 69, 69, 19, 6, 6, 6, 6, 1, 8, 8, 10, 10, 6, 6, 48, 48] 142 rigid atoms, others: [36, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 258 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113639 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 8, 8, 8, 26, 26, 26, 48, 48, 48, 83, 98, 99, 99, 99, 99, 48, 48, 26, 1, 1, 1, 5, 5, 5, 5, 5, 8, 26, 26, 26, 26, 48, 83, 83, 98, 98, 26, 26, 1, 1] 142 rigid atoms, others: [1, 2, 3, 4, 43, 44, 23, 24, 25] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 389 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113639 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [143, 101, 101, 67, 67, 67, 38, 38, 38, 16, 16, 16, 8, 4, 1, 1, 1, 1, 1, 1, 16, 16, 38, 101, 101, 101, 143, 143, 143, 143, 143, 67, 38, 38, 38, 38, 16, 8, 8, 4, 4, 38, 38, 101, 101] 143 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 511 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113639 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113639 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113639/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113639/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113639 Building REAL300020113640 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113640' /scratch/stefan/7770410/working/building/REAL300020113640 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300020113640 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113640/0 /scratch/stefan/7770410/working/building/REAL300020113640 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/889 `/scratch/stefan/7770410/working/3D/889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(C)[NH+]1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113640.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113640 none CC1CCC(C)[NH+]1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 22, 22, 18, 22, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 14, 14, 14, 14, 14, 14, 12, 12, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 18, 18, 6, 1, 1, 1, 1, 12, 14, 14, 14, 14, 1, 1] 82 rigid atoms, others: [11, 15, 44, 43, 12, 13, 14, 45, 52, 46, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 101 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113640 none CC1CCC(C)[NH+]1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 80, 80, 80, 78, 80, 34, 34, 34, 12, 12, 12, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 12, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 78, 78, 34, 12, 12, 12, 12, 1, 4, 4, 4, 4, 12, 12] 82 rigid atoms, others: [14, 47, 16, 17, 18, 25, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 298 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113640 none CC1CCC(C)[NH+]1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 22, 22, 22, 80, 80, 80, 82, 82, 82, 82, 82, 82, 80, 80, 22, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 13, 22, 22, 22, 22, 80, 82, 82, 82, 82, 22, 22] 82 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 7, 34, 35, 36, 5, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 169 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113640 none CC1CCC(C)[NH+]1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 82, 82, 82, 80, 82, 36, 36, 36, 14, 14, 14, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 80, 80, 36, 14, 14, 14, 14, 4, 3, 3, 1, 1, 14, 14] 82 rigid atoms, others: [19, 50, 18, 51, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 299 number of broken/clashed sets: 3 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113640 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113640 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 0: /scratch/stefan/7770410/working/building/REAL300020113640/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113640 Building REAL300020113641 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113641' /scratch/stefan/7770410/working/building/REAL300020113641 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113641 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113641/0 /scratch/stefan/7770410/working/building/REAL300020113641 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/890 `/scratch/stefan/7770410/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2=NN=CN2C1) `REAL300020113641.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113641 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2=NN=CN2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 8, 8, 1, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 12, 12, 12, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 12, 35, 101, 101, 101, 101, 101, 101, 101, 101, 35, 12, 12, 12, 12, 1, 7, 7, 9, 9, 12, 12, 101, 101, 101, 101, 101, 101, 101, 101] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 304 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113641 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2=NN=CN2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 8, 8, 1, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 59, 59, 59, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 59, 114, 201, 201, 201, 201, 201, 201, 201, 201, 114, 59, 59, 59, 59, 11, 6, 6, 4, 4, 59, 59, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 603 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113641 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2=NN=CN2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 8, 8, 1, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 35, 51, 59, 59, 59, 59, 12, 12, 1, 6, 24, 24, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 12, 35, 35, 51, 51, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113641 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2=NN=CN2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 8, 8, 1, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 9, 9, 24, 24, 24, 101, 101, 101, 158, 201, 201, 201, 201, 201, 101, 101, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 24, 24, 24, 24, 101, 158, 158, 201, 201, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 726 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113641 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113641/1 /scratch/stefan/7770410/working/building/REAL300020113641 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 891) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/891 `/scratch/stefan/7770410/working/3D/891' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2=NN=CN2C1) `REAL300020113641.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113641/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113641 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2=NN=CN2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 8, 8, 1, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 12, 12, 12, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 12, 36, 101, 101, 101, 101, 101, 101, 101, 101, 36, 12, 12, 12, 12, 1, 7, 7, 9, 9, 12, 12, 101, 101, 101, 101, 101, 101, 101, 101] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 306 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113641 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2=NN=CN2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 8, 8, 1, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 60, 60, 60, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 60, 114, 201, 201, 201, 201, 201, 201, 201, 201, 114, 60, 60, 60, 60, 11, 6, 6, 4, 4, 60, 60, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 603 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113641 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2=NN=CN2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 8, 8, 1, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 36, 52, 60, 60, 60, 60, 12, 12, 1, 6, 24, 24, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 12, 36, 36, 52, 52, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113641 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2=NN=CN2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 8, 8, 1, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 9, 9, 24, 24, 24, 101, 101, 101, 158, 201, 201, 201, 201, 201, 101, 101, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 24, 24, 24, 24, 101, 158, 158, 201, 201, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 726 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113641 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113641 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113641/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113641/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113641 Building REAL300020113642 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113642' /scratch/stefan/7770410/working/building/REAL300020113642 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113642 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113642/0 /scratch/stefan/7770410/working/building/REAL300020113642 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/892 `/scratch/stefan/7770410/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCN1C=C(Cl)C=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113642.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113642 none O=C(CCN1C=C(Cl)C=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 16, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 23, 26, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 9, 9, 9, 31, 43, 48, 48, 48, 48, 9, 9, 1, 23, 23, 26, 26, 35, 35, 6, 1, 1, 1, 1, 9, 31, 31, 43, 43, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 44, 10, 11, 12, 13, 14, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 292 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113642 none O=C(CCN1C=C(Cl)C=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 16, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 92, 94, 106, 106, 106, 106, 106, 9, 9, 9, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 9, 92, 92, 94, 94, 106, 106, 28, 9, 9, 9, 9, 1, 8, 8, 10, 10, 9, 9] 201 rigid atoms, others: [38, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 400 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113642 none O=C(CCN1C=C(Cl)C=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 16, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 9, 5, 1, 1, 1, 1, 1, 1, 1, 18, 18, 35, 35, 35, 106, 106, 106, 164, 201, 201, 201, 201, 201, 106, 106, 35, 9, 9, 5, 5, 1, 1, 18, 35, 35, 35, 35, 106, 164, 164, 201, 201, 35, 35] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 721 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113642 none O=C(CCN1C=C(Cl)C=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 16, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 192, 193, 201, 201, 201, 201, 201, 48, 48, 48, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 48, 192, 192, 193, 193, 201, 201, 101, 48, 48, 48, 48, 12, 6, 6, 4, 4, 48, 48] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 694 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113642 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113642/1 /scratch/stefan/7770410/working/building/REAL300020113642 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 893) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/893 `/scratch/stefan/7770410/working/3D/893' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCN1C=C(Cl)C=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113642.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113642 none O=C(CCN1C=C(Cl)C=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 16, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 23, 26, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 9, 9, 9, 31, 44, 49, 49, 49, 49, 9, 9, 1, 23, 23, 26, 26, 34, 34, 6, 1, 1, 1, 1, 9, 31, 31, 44, 44, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 44, 10, 11, 12, 13, 14, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 296 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113642 none O=C(CCN1C=C(Cl)C=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 16, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 92, 95, 107, 107, 107, 107, 107, 9, 9, 9, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 9, 92, 92, 95, 95, 107, 107, 29, 9, 9, 9, 9, 1, 8, 8, 10, 10, 9, 9] 201 rigid atoms, others: [38, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 407 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113642 none O=C(CCN1C=C(Cl)C=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 16, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 9, 5, 1, 1, 1, 1, 1, 1, 1, 18, 18, 34, 34, 34, 107, 107, 107, 165, 201, 201, 201, 201, 201, 107, 107, 34, 9, 9, 5, 5, 1, 1, 18, 34, 34, 34, 34, 107, 165, 165, 201, 201, 34, 34] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 715 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113642 none O=C(CCN1C=C(Cl)C=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 16, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 192, 193, 201, 201, 201, 201, 201, 49, 49, 49, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 49, 192, 192, 193, 193, 201, 201, 101, 49, 49, 49, 49, 12, 6, 6, 4, 4, 49, 49] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 694 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113642 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113642 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113642/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113642/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113642 Building REAL300020113643 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113643' /scratch/stefan/7770410/working/building/REAL300020113643 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113643 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113643/0 /scratch/stefan/7770410/working/building/REAL300020113643 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/894 `/scratch/stefan/7770410/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113643.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113643 none CCOCCOC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [129, 129, 109, 75, 45, 38, 22, 38, 22, 22, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 129, 129, 129, 129, 129, 109, 109, 75, 75, 38, 38, 38, 38, 22, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [45, 14, 13, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 571 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113643 none CCOCCOC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 200, 147, 83, 77, 58, 77, 58, 58, 35, 35, 35, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 35, 201, 201, 201, 201, 201, 200, 200, 147, 147, 77, 77, 77, 77, 58, 35, 35, 35, 35, 8, 4, 4, 2, 2, 35, 35] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 932 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113643 none CCOCCOC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 38, 25, 14, 10, 5, 10, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 24, 36, 37, 37, 37, 37, 8, 8, 1, 56, 56, 56, 56, 56, 38, 38, 25, 25, 10, 10, 10, 10, 5, 1, 1, 1, 1, 8, 24, 24, 36, 36, 1, 1] 201 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 44, 50, 51, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 349 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113643 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113643/1 /scratch/stefan/7770410/working/building/REAL300020113643 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 895) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/895 `/scratch/stefan/7770410/working/3D/895' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113643.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113643/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113643 none CCOCCOC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 107, 74, 45, 38, 22, 38, 22, 22, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 127, 127, 127, 127, 127, 107, 107, 74, 74, 38, 38, 38, 38, 22, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [45, 14, 13, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 562 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113643 none CCOCCOC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 200, 147, 83, 77, 58, 77, 58, 58, 35, 35, 35, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 35, 201, 201, 201, 201, 201, 200, 200, 147, 147, 77, 77, 77, 77, 58, 35, 35, 35, 35, 8, 4, 4, 2, 2, 35, 35] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 932 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113643 none CCOCCOC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 36, 25, 14, 10, 5, 10, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 24, 36, 37, 37, 37, 37, 8, 8, 1, 54, 54, 54, 54, 54, 36, 36, 25, 25, 10, 10, 10, 10, 5, 1, 1, 1, 1, 8, 24, 24, 36, 36, 1, 1] 201 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 44, 50, 51, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 337 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113643 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113643 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113643/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113643/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113643 Building REAL300020113644 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113644' /scratch/stefan/7770410/working/building/REAL300020113644 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113644 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113644/0 /scratch/stefan/7770410/working/building/REAL300020113644 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/896 `/scratch/stefan/7770410/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=CC2=CC=CC=C21) `REAL300020113644.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113644 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 7, 7, 7, 1, 1, 1, 1, 1, 9, 13, 18, 18, 18, 18, 1, 1, 7, 26, 87, 87, 87, 76, 87, 87, 87, 87, 87, 26, 7, 7, 7, 7, 1, 9, 9, 13, 13, 7, 7, 87, 87, 87, 87, 87, 87] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 239 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113644 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 57, 57, 57, 23, 23, 23, 8, 4, 1, 1, 1, 1, 1, 1, 23, 23, 57, 112, 201, 201, 201, 189, 201, 201, 201, 201, 201, 112, 57, 57, 57, 57, 23, 8, 8, 4, 4, 57, 57, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 471 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113644 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 31, 42, 53, 53, 53, 53, 7, 7, 1, 6, 37, 37, 37, 28, 37, 37, 37, 37, 37, 6, 1, 1, 1, 1, 7, 31, 31, 42, 42, 1, 1, 37, 37, 37, 37, 37, 37] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113644 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 37, 37, 37, 87, 87, 87, 163, 201, 201, 201, 201, 201, 87, 87, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 37, 37, 37, 37, 87, 163, 163, 201, 201, 37, 37, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 771 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113644 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113644/1 /scratch/stefan/7770410/working/building/REAL300020113644 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 897) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/897 `/scratch/stefan/7770410/working/3D/897' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=CC2=CC=CC=C21) `REAL300020113644.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113644 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 7, 7, 7, 1, 1, 1, 1, 1, 9, 13, 18, 18, 18, 18, 1, 1, 7, 26, 87, 87, 87, 76, 87, 87, 87, 87, 87, 26, 7, 7, 7, 7, 1, 9, 9, 13, 13, 7, 7, 87, 87, 87, 87, 87, 87] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 239 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113644 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 57, 57, 57, 23, 23, 23, 8, 4, 1, 1, 1, 1, 1, 1, 23, 23, 57, 113, 201, 201, 201, 189, 201, 201, 201, 201, 201, 113, 57, 57, 57, 57, 23, 8, 8, 4, 4, 57, 57, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 471 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113644 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 31, 42, 53, 53, 53, 53, 7, 7, 1, 6, 37, 37, 37, 28, 37, 37, 37, 37, 37, 6, 1, 1, 1, 1, 7, 31, 31, 42, 42, 1, 1, 37, 37, 37, 37, 37, 37] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113644 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 37, 37, 37, 87, 87, 87, 163, 201, 201, 201, 201, 201, 87, 87, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 37, 37, 37, 37, 87, 163, 163, 201, 201, 37, 37, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 771 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113644 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113644 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113644/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113644/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113644 Building REAL300020113645 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113645' /scratch/stefan/7770410/working/building/REAL300020113645 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113645 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113645/0 /scratch/stefan/7770410/working/building/REAL300020113645 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/898 `/scratch/stefan/7770410/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1) `REAL300020113645.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113645 none CN1C=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 47, 36, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 24, 37, 37, 37, 37, 37, 12, 12, 1, 80, 80, 80, 80, 80, 80, 47, 47, 36, 36, 6, 1, 1, 1, 1, 12, 24, 24, 37, 37, 1, 1, 80] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 45, 46, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47]) total number of confs: 403 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113645 none CN1C=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 173, 130, 120, 46, 46, 46, 12, 12, 12, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 12, 173, 173, 173, 173, 173, 173, 130, 130, 120, 120, 46, 12, 12, 12, 12, 1, 5, 5, 7, 7, 12, 12, 173] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 612 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113645 none CN1C=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 6, 26, 27, 27, 80, 80, 80, 173, 173, 173, 189, 201, 201, 201, 201, 201, 173, 173, 80, 1, 1, 2, 2, 2, 1, 2, 2, 7, 7, 27, 80, 80, 80, 80, 173, 189, 189, 201, 201, 80, 80, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 47, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 542 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113645 none CN1C=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 174, 165, 99, 99, 99, 42, 42, 42, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 42, 201, 201, 201, 201, 201, 201, 174, 174, 165, 165, 99, 42, 42, 42, 42, 9, 4, 4, 2, 2, 42, 42, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 681 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113645 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113645/1 /scratch/stefan/7770410/working/building/REAL300020113645 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 899) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/899 `/scratch/stefan/7770410/working/3D/899' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1) `REAL300020113645.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113645 none CN1C=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 47, 36, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 24, 37, 37, 37, 37, 37, 12, 12, 1, 80, 80, 80, 80, 80, 80, 47, 47, 36, 36, 6, 1, 1, 1, 1, 12, 24, 24, 37, 37, 1, 1, 80] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 45, 46, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47]) total number of confs: 403 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113645 none CN1C=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 173, 130, 120, 46, 46, 46, 12, 12, 12, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 12, 173, 173, 173, 173, 173, 173, 130, 130, 120, 120, 46, 12, 12, 12, 12, 1, 5, 5, 7, 7, 12, 12, 173] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 612 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113645 none CN1C=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 6, 26, 27, 27, 80, 80, 80, 173, 173, 173, 189, 201, 201, 201, 201, 201, 173, 173, 80, 1, 1, 2, 2, 2, 1, 2, 2, 7, 7, 27, 80, 80, 80, 80, 173, 189, 189, 201, 201, 80, 80, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 47, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 542 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113645 none CN1C=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 174, 165, 99, 99, 99, 42, 42, 42, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 42, 201, 201, 201, 201, 201, 201, 174, 174, 165, 165, 99, 42, 42, 42, 42, 9, 4, 4, 2, 2, 42, 42, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 681 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113645 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113645 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113645/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113645/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113645 Building REAL300020113646 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113646' /scratch/stefan/7770410/working/building/REAL300020113646 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113646 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113646/0 /scratch/stefan/7770410/working/building/REAL300020113646 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/900 `/scratch/stefan/7770410/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC[NH+]1CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113646.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113646 none O=C(CCC[NH+]1CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 10, 10, 10, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 10, 10, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1] 21 rigid atoms, others: [11, 15, 44, 43, 12, 13, 14, 45, 52, 46, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 73 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113646 none O=C(CCC[NH+]1CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 21, 21, 21, 21, 21, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 8, 13, 13, 13, 13, 13, 13, 21, 21, 21, 21, 21, 21, 21, 21, 13, 8, 8, 8, 8, 1, 3, 3, 3, 3, 8, 8] 21 rigid atoms, others: [14, 47, 16, 17, 18, 25, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 72 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113646 none O=C(CCC[NH+]1CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 6, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12, 17, 17, 17, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 17, 8, 8, 6, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 17, 17, 17, 17, 21, 21, 21, 21, 21, 17, 17] 21 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 39, 40, 41, 36, 38, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 73 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113646 none O=C(CCC[NH+]1CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 21, 21, 21, 21, 21, 8, 8, 8, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 14, 14, 14, 14, 14, 14, 21, 21, 21, 21, 21, 21, 21, 21, 14, 8, 8, 8, 8, 3, 3, 3, 1, 1, 8, 8] 21 rigid atoms, others: [19, 50, 18, 51, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 70 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113646 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113646/1 /scratch/stefan/7770410/working/building/REAL300020113646 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 901) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/901 `/scratch/stefan/7770410/working/3D/901' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC[NH+]1CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113646.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113646 none O=C(CCC[NH+]1CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 10, 10, 10, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 10, 10, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1] 21 rigid atoms, others: [11, 15, 44, 43, 12, 13, 14, 45, 52, 46, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 73 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113646 none O=C(CCC[NH+]1CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 21, 21, 21, 21, 21, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 8, 13, 13, 13, 13, 13, 13, 21, 21, 21, 21, 21, 21, 21, 21, 13, 8, 8, 8, 8, 1, 3, 3, 3, 3, 8, 8] 21 rigid atoms, others: [14, 47, 16, 17, 18, 25, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 72 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113646 none O=C(CCC[NH+]1CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 6, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12, 17, 17, 17, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 17, 8, 8, 6, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 17, 17, 17, 17, 21, 21, 21, 21, 21, 17, 17] 21 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 39, 40, 41, 36, 38, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 73 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113646 none O=C(CCC[NH+]1CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 21, 21, 21, 21, 21, 8, 8, 8, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 13, 13, 13, 13, 13, 13, 21, 21, 21, 21, 21, 21, 21, 21, 13, 8, 8, 8, 8, 3, 3, 3, 1, 1, 8, 8] 21 rigid atoms, others: [19, 50, 18, 51, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 70 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113646 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113646 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113646/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113646/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113646 Building REAL300020113647 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113647' /scratch/stefan/7770410/working/building/REAL300020113647 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113647 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113647/0 /scratch/stefan/7770410/working/building/REAL300020113647 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/902 `/scratch/stefan/7770410/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020113647.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113647 none C[NH+](C)CC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 53, 58, 58, 17, 17, 17, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 26, 28, 28, 28, 28, 28, 13, 13, 1, 17, 58, 58, 58, 58, 58, 58, 53, 53, 17, 17, 17, 6, 1, 1, 1, 1, 13, 26, 26, 28, 28, 1, 1, 17] 201 rigid atoms, others: [45, 44, 42, 43, 12, 13, 14, 15, 16, 51, 52, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50, 53]) total number of confs: 306 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113647 none C[NH+](C)CC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 163, 163, 163, 90, 90, 90, 90, 90, 49, 49, 49, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 13, 90, 163, 163, 163, 163, 163, 163, 163, 163, 90, 90, 90, 49, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 90] 201 rigid atoms, others: [46, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 628 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113647 none C[NH+](C)CC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 90, 90, 90, 124, 126, 126, 126, 126, 126, 90, 90, 17, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 5, 17, 17, 17, 17, 90, 124, 124, 126, 126, 17, 17, 1] 201 rigid atoms, others: [4, 5, 38, 7, 8, 9, 10, 39, 40, 53, 6, 29] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 373 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113647 none C[NH+](C)CC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 126, 126, 126, 126, 126, 73, 73, 73, 25, 25, 25, 7, 7, 7, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 25, 126, 201, 201, 201, 201, 201, 201, 201, 201, 126, 126, 126, 73, 25, 25, 25, 25, 7, 3, 3, 1, 1, 25, 25, 126] 201 rigid atoms, others: [49, 50, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 51, 52, 53]) total number of confs: 747 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113647 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113647/1 /scratch/stefan/7770410/working/building/REAL300020113647 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 903) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/903 `/scratch/stefan/7770410/working/3D/903' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020113647.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113647/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113647 none C[NH+](C)CC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 53, 58, 58, 17, 17, 17, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 26, 28, 28, 28, 28, 28, 13, 13, 1, 17, 58, 58, 58, 58, 58, 58, 53, 53, 17, 17, 17, 6, 1, 1, 1, 1, 13, 26, 26, 28, 28, 1, 1, 17] 201 rigid atoms, others: [45, 44, 42, 43, 12, 13, 14, 15, 16, 51, 52, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50, 53]) total number of confs: 306 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113647 none C[NH+](C)CC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 163, 163, 163, 90, 90, 90, 90, 90, 49, 49, 49, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 13, 90, 163, 163, 163, 163, 163, 163, 163, 163, 90, 90, 90, 49, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 90] 201 rigid atoms, others: [46, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 628 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113647 none C[NH+](C)CC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 90, 90, 90, 124, 126, 126, 126, 126, 126, 90, 90, 17, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 5, 17, 17, 17, 17, 90, 124, 124, 126, 126, 17, 17, 1] 201 rigid atoms, others: [4, 5, 38, 7, 8, 9, 10, 39, 40, 53, 6, 29] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 373 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113647 none C[NH+](C)CC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 126, 126, 126, 126, 126, 73, 73, 73, 25, 25, 25, 7, 7, 7, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 25, 126, 201, 201, 201, 201, 201, 201, 201, 201, 126, 126, 126, 73, 25, 25, 25, 25, 7, 3, 3, 1, 1, 25, 25, 126] 201 rigid atoms, others: [49, 50, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 51, 52, 53]) total number of confs: 747 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113647 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113647 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113647/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113647/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113647 Building REAL300020113648 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113648' /scratch/stefan/7770410/working/building/REAL300020113648 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113648 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113648/0 /scratch/stefan/7770410/working/building/REAL300020113648 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/904 `/scratch/stefan/7770410/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=NNC2=CC=CC=C21)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113648.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113648 none O=C(CC1=NNC2=CC=CC=C21)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 21, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 8, 8, 8, 27, 39, 41, 41, 41, 41, 8, 8, 1, 21, 21, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 8, 27, 27, 39, 39, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 46, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 247 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113648 none O=C(CC1=NNC2=CC=CC=C21)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 76, 98, 98, 98, 98, 98, 98, 98, 98, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 76, 76, 98, 98, 98, 98, 98, 25, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 343 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113648 none O=C(CC1=NNC2=CC=CC=C21)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 27, 27, 27, 98, 98, 98, 168, 201, 201, 201, 201, 201, 98, 98, 27, 4, 4, 1, 1, 1, 1, 1, 9, 27, 27, 27, 27, 98, 168, 168, 201, 201, 27, 27] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 737 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113648 none O=C(CC1=NNC2=CC=CC=C21)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 152, 201, 201, 201, 201, 201, 201, 201, 201, 41, 41, 41, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 41, 152, 152, 201, 201, 201, 201, 201, 77, 41, 41, 41, 41, 9, 5, 5, 3, 3, 41, 41] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 663 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113648 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113648/1 /scratch/stefan/7770410/working/building/REAL300020113648 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 905) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/905 `/scratch/stefan/7770410/working/3D/905' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=NNC2=CC=CC=C21)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113648.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113648 none O=C(CC1=NNC2=CC=CC=C21)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 21, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 8, 8, 8, 27, 39, 41, 41, 41, 41, 8, 8, 1, 21, 21, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 8, 27, 27, 39, 39, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 46, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 247 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113648 none O=C(CC1=NNC2=CC=CC=C21)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 76, 98, 98, 98, 98, 98, 98, 98, 98, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 76, 76, 98, 98, 98, 98, 98, 25, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 343 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113648 none O=C(CC1=NNC2=CC=CC=C21)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 27, 27, 27, 98, 98, 98, 168, 201, 201, 201, 201, 201, 98, 98, 27, 4, 4, 1, 1, 1, 1, 1, 9, 27, 27, 27, 27, 98, 168, 168, 201, 201, 27, 27] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 734 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113648 none O=C(CC1=NNC2=CC=CC=C21)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 152, 201, 201, 201, 201, 201, 201, 201, 201, 42, 42, 42, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 42, 152, 152, 201, 201, 201, 201, 201, 77, 42, 42, 42, 42, 10, 5, 5, 3, 3, 42, 42] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 661 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113648 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113648 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113648/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113648/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113648 Building REAL300020113649 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113649' /scratch/stefan/7770410/working/building/REAL300020113649 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113649 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113649/0 /scratch/stefan/7770410/working/building/REAL300020113649 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/906 `/scratch/stefan/7770410/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC(C)(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113649.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113649 none CNC(=O)NC(C)(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 77, 77, 77, 77, 41, 77, 77, 41, 41, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 100, 100, 100, 100, 77, 77, 77, 77, 77, 77, 77, 41, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 384 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113649 none CNC(=O)NC(C)(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 154, 201, 201, 154, 154, 64, 64, 64, 12, 12, 12, 7, 4, 1, 1, 1, 1, 1, 1, 12, 12, 64, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 154, 64, 64, 64, 64, 12, 7, 7, 4, 4, 64, 64] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 639 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113649 none CNC(=O)NC(C)(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 17, 17, 17, 17, 6, 17, 17, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 37, 55, 63, 63, 63, 63, 11, 11, 1, 21, 21, 21, 21, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 11, 37, 37, 55, 55, 1, 1] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 311 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113649 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113649/1 /scratch/stefan/7770410/working/building/REAL300020113649 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 907) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/907 `/scratch/stefan/7770410/working/3D/907' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC(C)(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113649.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113649/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113649 none CNC(=O)NC(C)(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 77, 77, 77, 77, 41, 77, 77, 41, 41, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 100, 100, 100, 100, 77, 77, 77, 77, 77, 77, 77, 41, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 384 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113649 none CNC(=O)NC(C)(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 154, 201, 201, 154, 154, 64, 64, 64, 12, 12, 12, 7, 4, 1, 1, 1, 1, 1, 1, 12, 12, 64, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 154, 64, 64, 64, 64, 12, 7, 7, 4, 4, 64, 64] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 639 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113649 none CNC(=O)NC(C)(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 17, 17, 17, 17, 6, 17, 17, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 37, 55, 63, 63, 63, 63, 11, 11, 1, 21, 21, 21, 21, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 11, 37, 37, 55, 55, 1, 1] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 311 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113649 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113649 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113649/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113649/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113649 Building REAL300020113650 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113650' /scratch/stefan/7770410/working/building/REAL300020113650 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113650 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113650/0 /scratch/stefan/7770410/working/building/REAL300020113650 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/908 `/scratch/stefan/7770410/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CS1) `REAL300020113650.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113650 none CCC1=NC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 15, 15, 15, 15, 4, 4, 4, 1, 1, 1, 1, 1, 7, 7, 7, 18, 30, 30, 30, 30, 30, 7, 7, 1, 15, 15, 36, 36, 36, 36, 36, 15, 15, 4, 1, 1, 1, 1, 7, 18, 18, 30, 30, 1, 1, 15] 201 rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 11, 12, 45, 44, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46]) total number of confs: 280 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113650 none CCC1=NC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 53, 53, 53, 53, 14, 14, 14, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 53, 53, 102, 102, 102, 102, 102, 53, 53, 14, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 53] 201 rigid atoms, others: [39, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 491 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113650 none CCC1=NC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 3, 7, 7, 7, 15, 15, 15, 53, 53, 53, 91, 120, 120, 120, 120, 120, 53, 53, 15, 1, 1, 5, 5, 5, 4, 4, 3, 3, 7, 15, 15, 15, 15, 53, 91, 91, 120, 120, 15, 15, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 46, 25, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 486 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113650 none CCC1=NC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 120, 120, 120, 120, 45, 45, 45, 30, 30, 30, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 30, 120, 120, 201, 201, 201, 201, 201, 120, 120, 45, 30, 30, 30, 30, 7, 4, 4, 2, 2, 30, 30, 120] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 953 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113650 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113650/1 /scratch/stefan/7770410/working/building/REAL300020113650 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 909) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/909 `/scratch/stefan/7770410/working/3D/909' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CS1) `REAL300020113650.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113650/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113650 none CCC1=NC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 15, 15, 15, 15, 4, 4, 4, 1, 1, 1, 1, 1, 7, 7, 7, 18, 30, 30, 30, 30, 30, 7, 7, 1, 15, 15, 36, 36, 36, 36, 36, 15, 15, 4, 1, 1, 1, 1, 7, 18, 18, 30, 30, 1, 1, 15] 201 rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 11, 12, 45, 44, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46]) total number of confs: 280 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113650 none CCC1=NC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 53, 53, 53, 53, 14, 14, 14, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 53, 53, 103, 103, 103, 103, 103, 53, 53, 14, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 53] 201 rigid atoms, others: [39, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 497 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113650 none CCC1=NC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 3, 7, 7, 7, 15, 15, 15, 53, 53, 53, 91, 120, 120, 120, 120, 120, 53, 53, 15, 1, 1, 5, 5, 5, 4, 4, 3, 3, 7, 15, 15, 15, 15, 53, 91, 91, 120, 120, 15, 15, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 46, 25, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 486 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113650 none CCC1=NC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 120, 120, 120, 120, 45, 45, 45, 30, 30, 30, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 30, 120, 120, 201, 201, 201, 201, 201, 120, 120, 45, 30, 30, 30, 30, 7, 4, 4, 2, 2, 30, 30, 120] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 953 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113650 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113650 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113650/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113650/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113650 Building REAL300020113651 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113651' /scratch/stefan/7770410/working/building/REAL300020113651 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113651 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113651/0 /scratch/stefan/7770410/working/building/REAL300020113651 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/910 `/scratch/stefan/7770410/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1) `REAL300020113651.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113651 none CC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 40, 24, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 25, 37, 40, 40, 40, 40, 8, 8, 1, 40, 40, 40, 40, 40, 40, 24, 24, 6, 1, 1, 1, 1, 8, 25, 25, 37, 37, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 260 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113651 none CC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 117, 117, 117, 84, 21, 21, 21, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 8, 117, 117, 117, 117, 117, 117, 84, 84, 21, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 383 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113651 none CC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 22, 22, 22, 40, 40, 40, 117, 117, 117, 172, 201, 201, 201, 201, 201, 117, 117, 40, 1, 2, 2, 2, 1, 1, 7, 7, 22, 40, 40, 40, 40, 117, 172, 172, 201, 201, 40, 40] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 688 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113651 none CC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 190, 68, 68, 68, 40, 40, 40, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 40, 201, 201, 201, 201, 201, 201, 190, 190, 68, 40, 40, 40, 40, 10, 6, 6, 4, 4, 40, 40] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 710 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113651 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113651/1 /scratch/stefan/7770410/working/building/REAL300020113651 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 911) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/911 `/scratch/stefan/7770410/working/3D/911' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1) `REAL300020113651.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113651/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113651 none CC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 40, 24, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 25, 37, 40, 40, 40, 40, 8, 8, 1, 40, 40, 40, 40, 40, 40, 24, 24, 6, 1, 1, 1, 1, 8, 25, 25, 37, 37, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 260 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113651 none CC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 118, 84, 21, 21, 21, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 8, 118, 118, 118, 118, 118, 118, 84, 84, 21, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 385 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113651 none CC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 22, 22, 22, 40, 40, 40, 118, 118, 118, 172, 201, 201, 201, 201, 201, 118, 118, 40, 1, 2, 2, 2, 1, 1, 7, 7, 22, 40, 40, 40, 40, 118, 172, 172, 201, 201, 40, 40] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 684 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113651 none CC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 190, 70, 70, 70, 41, 41, 41, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 41, 201, 201, 201, 201, 201, 201, 190, 190, 70, 41, 41, 41, 41, 11, 6, 6, 4, 4, 41, 41] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 707 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113651 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113651 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113651/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113651/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113651 Building REAL300020113652 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113652' /scratch/stefan/7770410/working/building/REAL300020113652 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113652 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113652/0 /scratch/stefan/7770410/working/building/REAL300020113652 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/912 `/scratch/stefan/7770410/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC[NH+]1CCCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113652.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113652 none O=C(CC[NH+]1CCCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 23, 29, 29, 29, 29, 28, 29, 29, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 23, 23, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1] 71 rigid atoms, others: [11, 15, 44, 43, 12, 13, 14, 45, 52, 46, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 128 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113652 none O=C(CC[NH+]1CCCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 67, 71, 71, 71, 71, 71, 71, 71, 10, 10, 10, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 10, 67, 67, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 26, 10, 10, 10, 10, 1, 3, 3, 3, 3, 10, 10] 71 rigid atoms, others: [14, 47, 16, 17, 18, 25, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 293 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113652 none O=C(CC[NH+]1CCCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [11, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 29, 29, 29, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 29, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 29, 29, 29, 29, 71, 71, 71, 71, 71, 29, 29] 71 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 39, 40, 35, 41, 36, 38, 37] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 146 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113652 none O=C(CC[NH+]1CCCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 55, 58, 58, 58, 58, 58, 58, 58, 9, 9, 9, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 55, 55, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 26, 9, 9, 9, 9, 3, 3, 3, 1, 1, 9, 9] 58 rigid atoms, others: [19, 50, 18, 51, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 226 number of broken/clashed sets: 3 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113652 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113652/1 /scratch/stefan/7770410/working/building/REAL300020113652 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 913) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/913 `/scratch/stefan/7770410/working/3D/913' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC[NH+]1CCCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113652.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113652 none O=C(CC[NH+]1CCCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 23, 29, 29, 29, 29, 28, 29, 29, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 23, 23, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1] 71 rigid atoms, others: [11, 15, 44, 43, 12, 13, 14, 45, 52, 46, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 128 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113652 none O=C(CC[NH+]1CCCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 67, 71, 71, 71, 71, 71, 71, 71, 10, 10, 10, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 10, 67, 67, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 26, 10, 10, 10, 10, 1, 3, 3, 3, 3, 10, 10] 71 rigid atoms, others: [14, 47, 16, 17, 18, 25, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 293 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113652 none O=C(CC[NH+]1CCCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [11, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 29, 29, 29, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 29, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 29, 29, 29, 29, 71, 71, 71, 71, 71, 29, 29] 71 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 39, 40, 35, 41, 36, 38, 37] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 146 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113652 none O=C(CC[NH+]1CCCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 55, 58, 58, 58, 58, 58, 58, 58, 9, 9, 9, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 55, 55, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 26, 9, 9, 9, 9, 3, 3, 3, 1, 1, 9, 9] 58 rigid atoms, others: [19, 50, 18, 51, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 226 number of broken/clashed sets: 3 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113652 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113652 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113652/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113652/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113652 Building REAL300020113653 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113653' /scratch/stefan/7770410/working/building/REAL300020113653 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113653 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113653/0 /scratch/stefan/7770410/working/building/REAL300020113653 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/914 `/scratch/stefan/7770410/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1) `REAL300020113653.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113653 none CC1=CN(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 33, 47, 54, 54, 54, 54, 10, 10, 1, 27, 27, 27, 27, 27, 27, 20, 20, 20, 20, 6, 1, 1, 1, 1, 10, 33, 33, 47, 47, 1, 1, 27] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 45, 46, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47]) total number of confs: 285 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113653 none CC1=CN(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 94, 94, 36, 36, 36, 10, 10, 10, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 10, 100, 100, 100, 100, 100, 100, 94, 94, 94, 94, 36, 10, 10, 10, 10, 1, 7, 7, 9, 9, 10, 10, 100] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 396 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113653 none CC1=CN(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 8, 12, 12, 12, 27, 27, 27, 100, 100, 100, 169, 201, 201, 201, 201, 201, 100, 100, 27, 1, 1, 2, 2, 2, 1, 5, 5, 8, 8, 12, 27, 27, 27, 27, 100, 169, 169, 201, 201, 27, 27, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 47, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 729 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113653 none CC1=CN(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 125, 125, 125, 55, 55, 55, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 55, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 125, 55, 55, 55, 55, 12, 6, 6, 4, 4, 55, 55, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 699 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113653 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113653/1 /scratch/stefan/7770410/working/building/REAL300020113653 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 915) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/915 `/scratch/stefan/7770410/working/3D/915' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1) `REAL300020113653.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113653 none CC1=CN(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 33, 47, 54, 54, 54, 54, 10, 10, 1, 27, 27, 27, 27, 27, 27, 20, 20, 20, 20, 6, 1, 1, 1, 1, 10, 33, 33, 47, 47, 1, 1, 27] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 45, 46, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47]) total number of confs: 285 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113653 none CC1=CN(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 94, 94, 36, 36, 36, 10, 10, 10, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 10, 101, 101, 101, 101, 101, 101, 94, 94, 94, 94, 36, 10, 10, 10, 10, 1, 7, 7, 9, 9, 10, 10, 101] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 398 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113653 none CC1=CN(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 8, 12, 12, 12, 27, 27, 27, 101, 101, 101, 169, 201, 201, 201, 201, 201, 101, 101, 27, 1, 1, 2, 2, 2, 1, 5, 5, 8, 8, 12, 27, 27, 27, 27, 101, 169, 169, 201, 201, 27, 27, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 47, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 728 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113653 none CC1=CN(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 127, 127, 127, 56, 56, 56, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 56, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 127, 56, 56, 56, 56, 13, 6, 6, 4, 4, 56, 56, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 698 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113653 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113653 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113653/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113653/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113653 Building REAL300020113654 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113654' /scratch/stefan/7770410/working/building/REAL300020113654 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113654 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113654/0 /scratch/stefan/7770410/working/building/REAL300020113654 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/916 `/scratch/stefan/7770410/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C2OC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CC2=C1) `REAL300020113654.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113654 none CC1=CC=C2OC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 62, 82, 100, 100, 100, 100, 13, 13, 1, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 62, 62, 82, 82, 1, 1, 16, 16] 201 rigid atoms, others: [45, 35, 36, 37, 38, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47]) total number of confs: 376 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113654 none CC1=CC=C2OC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 94, 94, 94, 53, 53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 9, 12, 18, 18, 18, 18, 1, 1, 13, 94, 94, 94, 94, 94, 94, 94, 94, 53, 13, 13, 13, 13, 1, 9, 9, 12, 12, 13, 13, 94, 94] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 255 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113654 none CC1=CC=C2OC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 94, 94, 94, 160, 201, 201, 201, 201, 201, 94, 94, 16, 1, 1, 1, 2, 2, 2, 1, 1, 6, 16, 16, 16, 16, 94, 160, 160, 201, 201, 16, 16, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 46, 47, 26, 27, 28, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 710 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113654 none CC1=CC=C2OC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 168, 168, 168, 101, 101, 101, 20, 20, 20, 6, 4, 1, 1, 1, 1, 1, 1, 20, 20, 101, 201, 201, 201, 201, 201, 201, 201, 201, 168, 101, 101, 101, 101, 20, 6, 6, 4, 4, 101, 101, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 519 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113654 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113654/1 /scratch/stefan/7770410/working/building/REAL300020113654 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 917) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/917 `/scratch/stefan/7770410/working/3D/917' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C2OC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CC2=C1) `REAL300020113654.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113654 none CC1=CC=C2OC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 62, 82, 100, 100, 100, 100, 13, 13, 1, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 62, 62, 82, 82, 1, 1, 16, 16] 201 rigid atoms, others: [45, 35, 36, 37, 38, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47]) total number of confs: 376 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113654 none CC1=CC=C2OC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 94, 94, 94, 53, 53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 9, 12, 18, 18, 18, 18, 1, 1, 13, 94, 94, 94, 94, 94, 94, 94, 94, 53, 13, 13, 13, 13, 1, 9, 9, 12, 12, 13, 13, 94, 94] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 255 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113654 none CC1=CC=C2OC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 94, 94, 94, 160, 201, 201, 201, 201, 201, 94, 94, 16, 1, 1, 1, 2, 2, 2, 1, 1, 6, 16, 16, 16, 16, 94, 160, 160, 201, 201, 16, 16, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 46, 47, 26, 27, 28, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 710 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113654 none CC1=CC=C2OC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 168, 168, 168, 101, 101, 101, 20, 20, 20, 6, 4, 1, 1, 1, 1, 1, 1, 20, 20, 101, 201, 201, 201, 201, 201, 201, 201, 201, 168, 101, 101, 101, 101, 20, 6, 6, 4, 4, 101, 101, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 519 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113654 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113654 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113654/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113654/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113654 Building REAL300020113655 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113655' /scratch/stefan/7770410/working/building/REAL300020113655 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113655 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113655/0 /scratch/stefan/7770410/working/building/REAL300020113655 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/918 `/scratch/stefan/7770410/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113655.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113655 none C[NH+](C)CC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 9, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 11, 16, 16, 6, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1] 25 rigid atoms, others: [45, 43, 44, 13, 14, 15, 16, 17, 52, 46, 29, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113655 none C[NH+](C)CC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 22, 25, 25, 19, 19, 19, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 22, 25, 25, 19, 8, 8, 8, 8, 1, 3, 3, 3, 3, 8, 8] 25 rigid atoms, others: [47, 16, 17, 18, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 81 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113655 none C[NH+](C)CC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 16, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 16, 16, 16, 16, 25, 25, 25, 25, 25, 16, 16] 25 rigid atoms, others: [11, 4, 5, 38, 7, 8, 9, 10, 39, 40, 41, 6] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113655 none C[NH+](C)CC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 22, 25, 25, 19, 19, 19, 8, 8, 8, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 22, 25, 25, 19, 8, 8, 8, 8, 3, 3, 3, 1, 1, 8, 8] 25 rigid atoms, others: [50, 51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 79 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113655 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113655/1 /scratch/stefan/7770410/working/building/REAL300020113655 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 919) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/919 `/scratch/stefan/7770410/working/3D/919' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113655.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113655 none C[NH+](C)CC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 9, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 11, 16, 16, 6, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1] 25 rigid atoms, others: [45, 43, 44, 13, 14, 15, 16, 17, 52, 46, 29, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113655 none C[NH+](C)CC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 22, 25, 25, 19, 19, 19, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 22, 25, 25, 19, 8, 8, 8, 8, 1, 3, 3, 3, 3, 8, 8] 25 rigid atoms, others: [47, 16, 17, 18, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 81 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113655 none C[NH+](C)CC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 16, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 16, 16, 16, 16, 25, 25, 25, 25, 25, 16, 16] 25 rigid atoms, others: [11, 4, 5, 38, 7, 8, 9, 10, 39, 40, 41, 6] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113655 none C[NH+](C)CC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 22, 25, 25, 19, 19, 19, 8, 8, 8, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 22, 25, 25, 19, 8, 8, 8, 8, 3, 3, 3, 1, 1, 8, 8] 25 rigid atoms, others: [50, 51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 79 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113655 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113655 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113655/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113655/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113655 Building REAL300020113656 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113656' /scratch/stefan/7770410/working/building/REAL300020113656 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113656 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113656/0 /scratch/stefan/7770410/working/building/REAL300020113656 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/920 `/scratch/stefan/7770410/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113656.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113656 none CCS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 111, 98, 111, 111, 36, 36, 36, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 112, 112, 112, 112, 112, 98, 98, 36, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 465 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113656 none CCS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 198, 201, 201, 96, 96, 96, 47, 47, 47, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 47, 201, 201, 201, 201, 201, 198, 198, 96, 47, 47, 47, 47, 10, 6, 6, 4, 4, 47, 47] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 772 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113656 none CCS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 34, 23, 34, 34, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 47, 51, 51, 51, 51, 11, 11, 1, 35, 35, 35, 35, 35, 23, 23, 6, 1, 1, 1, 1, 11, 33, 33, 47, 47, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113656 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113656/1 /scratch/stefan/7770410/working/building/REAL300020113656 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 921) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/921 `/scratch/stefan/7770410/working/3D/921' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113656.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113656 none CCS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 112, 99, 112, 112, 37, 37, 37, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 113, 113, 113, 113, 113, 99, 99, 37, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 467 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113656 none CCS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 198, 201, 201, 97, 97, 97, 47, 47, 47, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 47, 201, 201, 201, 201, 201, 198, 198, 97, 47, 47, 47, 47, 10, 6, 6, 4, 4, 47, 47] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 773 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113656 none CCS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 34, 23, 34, 34, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 47, 51, 51, 51, 51, 11, 11, 1, 35, 35, 35, 35, 35, 23, 23, 6, 1, 1, 1, 1, 11, 33, 33, 47, 47, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113656 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113656 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113656/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113656/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113656 Building REAL300020113657 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113657' /scratch/stefan/7770410/working/building/REAL300020113657 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113657 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113657/0 /scratch/stefan/7770410/working/building/REAL300020113657 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/922 `/scratch/stefan/7770410/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=N1) `REAL300020113657.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113657 none NC(=O)CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 59, 101, 19, 19, 19, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 33, 40, 53, 53, 53, 53, 7, 7, 1, 19, 19, 101, 101, 59, 59, 19, 5, 1, 1, 1, 1, 7, 33, 33, 40, 40, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 496 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113657 none NC(=O)CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [136, 90, 136, 36, 36, 36, 19, 19, 19, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 18, 18, 18, 18, 1, 1, 7, 36, 36, 136, 136, 90, 90, 36, 19, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7] 201 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 523 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113657 none NC(=O)CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 8, 35, 1, 1, 1, 1, 1, 7, 7, 7, 19, 19, 19, 36, 36, 36, 96, 113, 133, 133, 133, 133, 36, 36, 19, 1, 1, 35, 35, 8, 8, 1, 7, 19, 19, 19, 19, 36, 96, 96, 113, 113, 19, 19] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 26, 27] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 562 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113657 none NC(=O)CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 201, 146, 146, 146, 104, 104, 104, 68, 68, 68, 27, 27, 27, 6, 4, 1, 1, 1, 1, 1, 1, 27, 27, 68, 146, 146, 201, 201, 200, 200, 146, 104, 68, 68, 68, 68, 27, 6, 6, 4, 4, 68, 68] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 662 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113657 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113657/1 /scratch/stefan/7770410/working/building/REAL300020113657 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 923) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/923 `/scratch/stefan/7770410/working/3D/923' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=N1) `REAL300020113657.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113657/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113657 none NC(=O)CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 60, 102, 19, 19, 19, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 32, 39, 52, 52, 52, 52, 7, 7, 1, 19, 19, 102, 102, 60, 60, 19, 5, 1, 1, 1, 1, 7, 32, 32, 39, 39, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 499 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113657 none NC(=O)CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [136, 91, 136, 36, 36, 36, 19, 19, 19, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 17, 17, 17, 17, 1, 1, 7, 36, 36, 136, 136, 91, 91, 36, 19, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7] 201 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 525 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113657 none NC(=O)CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 8, 35, 1, 1, 1, 1, 1, 7, 7, 7, 19, 19, 19, 36, 36, 36, 97, 114, 135, 135, 135, 135, 36, 36, 19, 1, 1, 35, 35, 8, 8, 1, 7, 19, 19, 19, 19, 36, 97, 97, 114, 114, 19, 19] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 26, 27] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 564 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113657 none NC(=O)CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 201, 148, 148, 148, 106, 106, 106, 69, 69, 69, 27, 27, 27, 6, 4, 1, 1, 1, 1, 1, 1, 27, 27, 69, 148, 148, 201, 201, 200, 200, 148, 106, 69, 69, 69, 69, 27, 6, 6, 4, 4, 69, 69] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 659 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113657 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113657 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113657/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113657/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113657 Building REAL300020113658 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113658' /scratch/stefan/7770410/working/building/REAL300020113658 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113658 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113658/0 /scratch/stefan/7770410/working/building/REAL300020113658 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/924 `/scratch/stefan/7770410/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1) `REAL300020113658.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113658 none CC(C)(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 70, 102, 38, 38, 38, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 102, 103, 103, 102, 103, 103, 102, 102, 102, 102, 102, 102, 70, 70, 38, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 103, 103, 103, 103, 103] 201 rigid atoms, others: [9, 42, 11, 12, 13, 20, 21, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 493 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113658 none CC(C)(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 171, 201, 121, 121, 121, 56, 56, 56, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 56, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 171, 171, 121, 56, 56, 56, 56, 11, 6, 6, 4, 4, 56, 56, 201, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 802 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113658 none CC(C)(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 13, 25, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 35, 50, 56, 56, 56, 56, 11, 11, 1, 25, 27, 27, 25, 27, 27, 25, 25, 25, 25, 25, 25, 13, 13, 6, 1, 1, 1, 1, 11, 35, 35, 50, 50, 1, 1, 27, 27, 27, 27, 27] 201 rigid atoms, others: [6, 38, 7, 8, 9, 10, 39, 47, 48, 40, 22, 41] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50, 51, 52, 53]) total number of confs: 332 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113658 none CC(C)(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 7, 11, 11, 11, 27, 27, 27, 103, 103, 103, 169, 201, 201, 201, 201, 201, 103, 103, 27, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 7, 7, 11, 27, 27, 27, 27, 103, 169, 169, 201, 201, 27, 27, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 49, 50, 51, 52, 53, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 731 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113658 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113658/1 /scratch/stefan/7770410/working/building/REAL300020113658 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 925) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/925 `/scratch/stefan/7770410/working/3D/925' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1) `REAL300020113658.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113658 none CC(C)(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 70, 103, 38, 38, 38, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 103, 104, 104, 103, 104, 104, 103, 103, 103, 103, 103, 103, 70, 70, 38, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 104, 104, 104, 104, 104] 201 rigid atoms, others: [9, 42, 11, 12, 13, 20, 21, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 499 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113658 none CC(C)(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 172, 201, 122, 122, 122, 57, 57, 57, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 57, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 172, 172, 122, 57, 57, 57, 57, 12, 6, 6, 4, 4, 57, 57, 201, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 797 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113658 none CC(C)(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 13, 25, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 35, 50, 56, 56, 56, 56, 11, 11, 1, 25, 27, 27, 25, 27, 27, 25, 25, 25, 25, 25, 25, 13, 13, 6, 1, 1, 1, 1, 11, 35, 35, 50, 50, 1, 1, 27, 27, 27, 27, 27] 201 rigid atoms, others: [6, 38, 7, 8, 9, 10, 39, 47, 48, 40, 22, 41] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50, 51, 52, 53]) total number of confs: 332 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113658 none CC(C)(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 7, 11, 11, 11, 27, 27, 27, 104, 104, 104, 169, 201, 201, 201, 201, 201, 104, 104, 27, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 7, 7, 11, 27, 27, 27, 27, 104, 169, 169, 201, 201, 27, 27, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 49, 50, 51, 52, 53, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 726 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113658 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113658 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113658/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113658/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113658 Building REAL300020113659 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113659' /scratch/stefan/7770410/working/building/REAL300020113659 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113659 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113659/0 /scratch/stefan/7770410/working/building/REAL300020113659 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/926 `/scratch/stefan/7770410/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+]1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113659.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113659 none CC[N@@H+]1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 10, 10, 10, 10, 10, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1] 23 rigid atoms, others: [11, 15, 44, 43, 12, 13, 14, 45, 52, 46, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 43 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113659 none CC[N@@H+]1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 14, 14, 14, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 14, 8, 8, 8, 8, 1, 3, 3, 3, 3, 8, 8] 23 rigid atoms, others: [14, 47, 16, 17, 18, 25, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 84 number of broken/clashed sets: 23 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113659 none CC[N@@H+]1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 23, 23, 23, 23, 23, 8, 8] 23 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 8, 9, 7, 34, 40, 35, 41, 36, 38, 39, 37] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 52 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113659 none CC[N@@H+]1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 15, 15, 15, 10, 10, 10, 5, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 5, 5, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 15, 10, 10, 10, 10, 5, 5, 5, 2, 2, 10, 10] 23 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 86 number of broken/clashed sets: 23 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113659 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113659/1 /scratch/stefan/7770410/working/building/REAL300020113659 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 927) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/927 `/scratch/stefan/7770410/working/3D/927' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+]1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113659.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113659 none CC[N@H+]1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [10, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 10, 10, 10, 10, 10, 10, 9, 9, 1, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 9, 10, 10, 10, 10, 1, 1] 27 rigid atoms, others: [11, 15, 44, 43, 12, 13, 14, 45, 52, 46, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 44 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113659 none CC[N@H+]1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 21, 21, 21, 9, 9, 9, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 21, 9, 9, 9, 9, 1, 4, 4, 4, 4, 9, 9] 27 rigid atoms, others: [14, 47, 16, 17, 18, 25, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 87 number of broken/clashed sets: 21 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113659 none CC[N@H+]1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 9, 9, 9, 26, 26, 26, 27, 27, 27, 27, 27, 27, 26, 26, 9, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 9, 9, 9, 9, 26, 27, 27, 27, 27, 9, 9] 27 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 8, 9, 7, 34, 40, 35, 41, 36, 38, 39, 37] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 61 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113659 none CC[N@H+]1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 22, 22, 22, 12, 12, 12, 6, 6, 6, 5, 2, 1, 1, 1, 1, 1, 1, 6, 6, 12, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 22, 12, 12, 12, 12, 6, 5, 5, 2, 2, 12, 12] 27 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 90 number of broken/clashed sets: 21 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113659 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113659 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113659/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113659/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113659 Building REAL300020113660 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113660' /scratch/stefan/7770410/working/building/REAL300020113660 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113660 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113660/0 /scratch/stefan/7770410/working/building/REAL300020113660 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/928 `/scratch/stefan/7770410/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@H]1CCCO1) `REAL300020113660.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113660 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 56, 162, 162, 162, 162, 162, 56, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 162, 162, 162, 162, 162, 162] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 473 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113660 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 46, 46, 46, 9, 9, 9, 5, 2, 1, 1, 1, 1, 1, 1, 9, 9, 46, 133, 201, 201, 201, 201, 201, 133, 46, 46, 46, 46, 9, 5, 5, 2, 2, 46, 46, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 610 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113660 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 28, 42, 42, 42, 42, 42, 13, 13, 1, 6, 45, 45, 45, 45, 45, 6, 1, 1, 1, 1, 13, 28, 28, 42, 42, 1, 1, 45, 45, 45, 45, 45, 45] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 35, 36, 26, 27, 28, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42]) total number of confs: 276 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113660 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 45, 45, 45, 162, 162, 162, 195, 201, 201, 201, 201, 201, 162, 162, 45, 1, 1, 1, 1, 1, 1, 12, 45, 45, 45, 45, 162, 195, 195, 201, 201, 45, 45, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 37, 38, 39, 40, 41, 42, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 490 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113660 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113660/1 /scratch/stefan/7770410/working/building/REAL300020113660 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 929) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/929 `/scratch/stefan/7770410/working/3D/929' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@H]1CCCO1) `REAL300020113660.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113660/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113660 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 57, 162, 162, 162, 162, 162, 57, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 162, 162, 162, 162, 162, 162] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 473 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113660 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 46, 46, 46, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 46, 133, 201, 201, 201, 201, 201, 133, 46, 46, 46, 46, 9, 5, 5, 2, 2, 46, 46, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 600 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113660 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 29, 43, 43, 43, 43, 43, 13, 13, 1, 6, 46, 46, 46, 46, 46, 6, 1, 1, 1, 1, 13, 29, 29, 43, 43, 1, 1, 46, 46, 46, 46, 46, 46] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 35, 36, 26, 27, 28, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42]) total number of confs: 284 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113660 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 46, 46, 46, 162, 162, 162, 192, 201, 201, 201, 201, 201, 162, 162, 46, 1, 1, 1, 1, 1, 1, 12, 46, 46, 46, 46, 162, 192, 192, 201, 201, 46, 46, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 37, 38, 39, 40, 41, 42, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 492 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113660 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113660 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113660/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113660/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113660 Building REAL300020113661 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113661' /scratch/stefan/7770410/working/building/REAL300020113661 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113661 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113661/0 /scratch/stefan/7770410/working/building/REAL300020113661 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/930 `/scratch/stefan/7770410/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C2(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)CC2)=C1) `REAL300020113661.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113661 none CC1=CC=CC(C2(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)CC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 1, 1, 1, 10, 10, 10, 26, 26, 26, 97, 97, 97, 100, 105, 105, 105, 105, 105, 97, 97, 26, 1, 1, 3, 3, 3, 3, 3, 3, 3, 10, 26, 26, 26, 26, 97, 100, 100, 105, 105, 26, 26, 1, 1, 1, 1, 3] 201 rigid atoms, others: [5, 6, 7, 47, 48, 49, 50, 26, 27] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51]) total number of confs: 210 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113661 none CC1=CC=CC(C2(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)CC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 108, 50, 50, 50, 22, 22, 22, 5, 5, 5, 4, 2, 1, 1, 1, 1, 1, 1, 5, 5, 22, 108, 108, 201, 201, 201, 201, 201, 201, 201, 50, 22, 22, 22, 22, 5, 4, 4, 2, 2, 22, 22, 108, 108, 108, 108, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 504 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113661 none CC1=CC=CC(C2(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)CC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 51, 51, 26, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 17, 19, 19, 19, 19, 19, 13, 13, 1, 26, 26, 51, 51, 51, 51, 51, 51, 51, 6, 1, 1, 1, 1, 13, 17, 17, 19, 19, 1, 1, 26, 26, 26, 26, 51] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51]) total number of confs: 162 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113661 none CC1=CC=CC(C2(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)CC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 19, 19, 19, 51, 51, 51, 188, 188, 188, 194, 201, 201, 201, 201, 201, 188, 188, 51, 3, 3, 1, 2, 2, 2, 1, 1, 1, 19, 51, 51, 51, 51, 188, 194, 194, 201, 201, 51, 51, 3, 3, 3, 3, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 51, 28, 5] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 398 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113661 none CC1=CC=CC(C2(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)CC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [188, 188, 188, 188, 188, 97, 41, 41, 41, 13, 13, 13, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 1, 1, 13, 97, 97, 188, 188, 188, 188, 188, 188, 188, 41, 13, 13, 13, 13, 1, 3, 3, 5, 5, 13, 13, 97, 97, 97, 97, 188] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 464 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113661 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113661/1 /scratch/stefan/7770410/working/building/REAL300020113661 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 931) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/931 `/scratch/stefan/7770410/working/3D/931' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C2(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)CC2)=C1) `REAL300020113661.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113661 none CC1=CC=CC(C2(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)CC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 1, 1, 1, 10, 10, 10, 26, 26, 26, 97, 97, 97, 100, 105, 105, 105, 105, 105, 97, 97, 26, 1, 1, 3, 3, 3, 3, 3, 3, 3, 10, 26, 26, 26, 26, 97, 100, 100, 105, 105, 26, 26, 1, 1, 1, 1, 3] 201 rigid atoms, others: [5, 6, 7, 47, 48, 49, 50, 26, 27] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51]) total number of confs: 210 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113661 none CC1=CC=CC(C2(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)CC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 108, 50, 50, 50, 22, 22, 22, 5, 5, 5, 4, 2, 1, 1, 1, 1, 1, 1, 5, 5, 22, 108, 108, 201, 201, 201, 201, 201, 201, 201, 50, 22, 22, 22, 22, 5, 4, 4, 2, 2, 22, 22, 108, 108, 108, 108, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 504 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113661 none CC1=CC=CC(C2(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)CC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 51, 51, 26, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 17, 19, 19, 19, 19, 19, 13, 13, 1, 26, 26, 51, 51, 51, 51, 51, 51, 51, 6, 1, 1, 1, 1, 13, 17, 17, 19, 19, 1, 1, 26, 26, 26, 26, 51] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51]) total number of confs: 162 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113661 none CC1=CC=CC(C2(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)CC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 19, 19, 19, 51, 51, 51, 188, 188, 188, 194, 201, 201, 201, 201, 201, 188, 188, 51, 3, 3, 1, 2, 2, 2, 1, 1, 1, 19, 51, 51, 51, 51, 188, 194, 194, 201, 201, 51, 51, 3, 3, 3, 3, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 51, 28, 5] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 398 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113661 none CC1=CC=CC(C2(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)CC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [188, 188, 188, 188, 188, 97, 41, 41, 41, 13, 13, 13, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 1, 1, 13, 97, 97, 188, 188, 188, 188, 188, 188, 188, 41, 13, 13, 13, 13, 1, 3, 3, 5, 5, 13, 13, 97, 97, 97, 97, 188] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 464 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113661 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113661 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113661/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113661/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113661 Building REAL300020113662 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113662' /scratch/stefan/7770410/working/building/REAL300020113662 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113662 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113662/0 /scratch/stefan/7770410/working/building/REAL300020113662 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/932 `/scratch/stefan/7770410/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1) `REAL300020113662.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113662 none CN(C)C(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 85, 93, 49, 49, 49, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 11, 85, 87, 87, 85, 87, 87, 93, 93, 93, 93, 93, 93, 85, 49, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 87, 87, 87, 87, 87] 201 rigid atoms, others: [9, 10, 11, 12, 13, 20, 21, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 392 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113662 none CN(C)C(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 151, 151, 151, 72, 72, 72, 14, 14, 14, 4, 4, 1, 1, 1, 1, 1, 1, 14, 14, 72, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 151, 72, 72, 72, 72, 14, 4, 4, 4, 4, 72, 72, 201, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 680 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113662 none CN(C)C(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 15, 21, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 53, 68, 81, 81, 81, 81, 11, 11, 1, 15, 17, 17, 15, 17, 17, 21, 21, 21, 21, 21, 21, 15, 6, 1, 1, 1, 1, 11, 53, 53, 68, 68, 1, 1, 17, 17, 17, 17, 17] 201 rigid atoms, others: [37, 6, 7, 8, 9, 10, 39, 46, 47, 40, 22, 38] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50, 51, 52]) total number of confs: 376 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113662 none CN(C)C(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 3, 4, 1, 3, 5, 5, 5, 17, 17, 17, 87, 87, 87, 172, 201, 201, 201, 201, 201, 87, 87, 17, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 3, 5, 17, 17, 17, 17, 87, 172, 172, 201, 201, 17, 17, 1, 1, 1, 1, 1] 201 rigid atoms, others: [3, 48, 49, 50, 51, 52, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 728 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113662 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113662/1 /scratch/stefan/7770410/working/building/REAL300020113662 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 933) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/933 `/scratch/stefan/7770410/working/3D/933' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1) `REAL300020113662.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113662/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113662 none CN(C)C(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 88, 96, 49, 49, 49, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 11, 88, 89, 89, 88, 89, 89, 96, 96, 96, 96, 96, 96, 88, 49, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 89, 89, 89, 89, 89] 201 rigid atoms, others: [9, 10, 11, 12, 13, 20, 21, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 399 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113662 none CN(C)C(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 151, 151, 151, 73, 73, 73, 15, 15, 15, 4, 4, 1, 1, 1, 1, 1, 1, 15, 15, 73, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 151, 73, 73, 73, 73, 15, 4, 4, 4, 4, 73, 73, 201, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 679 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113662 none CN(C)C(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 15, 22, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 55, 70, 83, 83, 83, 83, 11, 11, 1, 15, 17, 17, 15, 17, 17, 22, 22, 22, 22, 22, 22, 15, 6, 1, 1, 1, 1, 11, 55, 55, 70, 70, 1, 1, 17, 17, 17, 17, 17] 201 rigid atoms, others: [37, 6, 7, 8, 9, 10, 39, 46, 47, 40, 22, 38] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50, 51, 52]) total number of confs: 386 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113662 none CN(C)C(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 3, 4, 1, 3, 5, 5, 5, 17, 17, 17, 89, 89, 89, 173, 201, 201, 201, 201, 201, 89, 89, 17, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 3, 5, 17, 17, 17, 17, 89, 173, 173, 201, 201, 17, 17, 1, 1, 1, 1, 1] 201 rigid atoms, others: [3, 48, 49, 50, 51, 52, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 718 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113662 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113662 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113662/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113662/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113662 Building REAL300020113663 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113663' /scratch/stefan/7770410/working/building/REAL300020113663 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113663 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113663/0 /scratch/stefan/7770410/working/building/REAL300020113663 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/934 `/scratch/stefan/7770410/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(Cl)=NN1) `REAL300020113663.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113663 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(Cl)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'Cl', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 16, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 29, 42, 43, 43, 43, 43, 9, 9, 1, 17, 17, 17, 17, 32, 32, 32, 32, 32, 6, 1, 1, 1, 1, 9, 29, 29, 42, 42, 1, 1, 17] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 280 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113663 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(Cl)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'Cl', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 16, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 70, 70, 29, 29, 29, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 9, 70, 70, 70, 70, 107, 107, 107, 107, 107, 29, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 70] 201 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 381 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113663 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(Cl)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'Cl', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 16, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 70, 70, 70, 124, 168, 169, 169, 169, 169, 70, 70, 17, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 70, 124, 124, 168, 168, 17, 17, 1] 201 rigid atoms, others: [1, 2, 3, 4, 44, 23, 24, 25, 26] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 650 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113663 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(Cl)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'Cl', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 16, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 177, 177, 102, 102, 102, 62, 62, 62, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 62, 177, 177, 177, 177, 201, 201, 201, 201, 201, 102, 62, 62, 62, 62, 15, 6, 6, 4, 4, 62, 62, 177] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 566 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113663 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113663/1 /scratch/stefan/7770410/working/building/REAL300020113663 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 935) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/935 `/scratch/stefan/7770410/working/3D/935' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(Cl)=NN1) `REAL300020113663.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113663 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(Cl)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'Cl', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 16, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 30, 43, 44, 44, 44, 44, 9, 9, 1, 17, 17, 17, 17, 32, 32, 32, 32, 32, 6, 1, 1, 1, 1, 9, 30, 30, 43, 43, 1, 1, 17] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 283 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113663 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(Cl)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'Cl', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 16, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 69, 69, 28, 28, 28, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 9, 69, 69, 69, 69, 106, 106, 106, 106, 106, 28, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 69] 201 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 379 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113663 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(Cl)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'Cl', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 16, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 69, 69, 69, 125, 169, 170, 170, 170, 170, 69, 69, 17, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 69, 125, 125, 169, 169, 17, 17, 1] 201 rigid atoms, others: [1, 2, 3, 4, 44, 23, 24, 25, 26] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 657 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113663 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(Cl)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'Cl', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 16, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 177, 177, 102, 102, 102, 62, 62, 62, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 62, 177, 177, 177, 177, 201, 201, 201, 201, 201, 102, 62, 62, 62, 62, 15, 6, 6, 4, 4, 62, 62, 177] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 561 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113663 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113663 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113663/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113663/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113663 Building REAL300020113664 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113664' /scratch/stefan/7770410/working/building/REAL300020113664 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113664 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113664/0 /scratch/stefan/7770410/working/building/REAL300020113664 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/936 `/scratch/stefan/7770410/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1COCCC1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113664.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113664 none COC1COCCC1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 31, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 26, 34, 34, 34, 34, 34, 13, 13, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 31, 31, 6, 1, 1, 1, 1, 13, 26, 26, 34, 34, 1, 1] 201 rigid atoms, others: [45, 43, 44, 42, 11, 12, 13, 14, 15, 51, 52, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50]) total number of confs: 263 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113664 none COC1COCCC1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 156, 156, 156, 156, 156, 145, 54, 54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 145, 145, 54, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [46, 15, 16, 17, 18, 14, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 591 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113664 none COC1COCCC1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 40, 40, 40, 156, 156, 156, 183, 201, 201, 201, 201, 201, 156, 156, 40, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 40, 40, 40, 40, 156, 183, 183, 201, 201, 40, 40] 201 rigid atoms, others: [32, 1, 2, 3, 4, 33, 6, 7, 8, 34, 35, 36, 38, 5, 37, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 515 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113664 none COC1COCCC1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 199, 110, 110, 110, 38, 38, 38, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 38, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 199, 199, 110, 38, 38, 38, 38, 8, 4, 4, 2, 2, 38, 38] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 718 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113664 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113664/1 /scratch/stefan/7770410/working/building/REAL300020113664 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 937) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/937 `/scratch/stefan/7770410/working/3D/937' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1COCCC1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113664.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113664 none COC1COCCC1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 31, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 25, 33, 33, 33, 33, 33, 13, 13, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 31, 31, 6, 1, 1, 1, 1, 13, 25, 25, 33, 33, 1, 1] 201 rigid atoms, others: [45, 43, 44, 42, 11, 12, 13, 14, 15, 51, 52, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50]) total number of confs: 260 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113664 none COC1COCCC1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 156, 156, 156, 156, 156, 145, 54, 54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 13, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 145, 145, 54, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13] 201 rigid atoms, others: [46, 15, 16, 17, 18, 14, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 588 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113664 none COC1COCCC1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 40, 40, 40, 156, 156, 156, 183, 201, 201, 201, 201, 201, 156, 156, 40, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 40, 40, 40, 40, 156, 183, 183, 201, 201, 40, 40] 201 rigid atoms, others: [32, 1, 2, 3, 4, 33, 6, 7, 8, 34, 35, 36, 38, 5, 37, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 515 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113664 none COC1COCCC1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 199, 111, 111, 111, 40, 40, 40, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 40, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 199, 199, 111, 40, 40, 40, 40, 8, 4, 4, 2, 2, 40, 40] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 718 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113664 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113664 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113664/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113664/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113664 Building REAL300020113665 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113665' /scratch/stefan/7770410/working/building/REAL300020113665 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113665 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113665/0 /scratch/stefan/7770410/working/building/REAL300020113665 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/938 `/scratch/stefan/7770410/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1(C(F)(F)F)CC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113665.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113665 none O=C(CC1(C(F)(F)F)CC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 15, 15, 15, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 22, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 11, 11, 11, 28, 43, 45, 45, 45, 45, 11, 11, 1, 22, 22, 33, 33, 33, 33, 6, 1, 1, 1, 1, 11, 28, 28, 43, 43, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 44, 10, 11, 12, 13, 14, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 289 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113665 none O=C(CC1(C(F)(F)F)CC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 15, 15, 15, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 90, 111, 111, 111, 111, 111, 111, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 90, 90, 111, 111, 111, 111, 33, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [38, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 427 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113665 none O=C(CC1(C(F)(F)F)CC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 15, 15, 15, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 1, 1, 1, 2, 2, 2, 1, 1, 15, 15, 33, 33, 33, 111, 111, 111, 168, 201, 201, 201, 201, 201, 111, 111, 33, 5, 5, 1, 1, 1, 1, 15, 33, 33, 33, 33, 111, 168, 168, 201, 201, 33, 33] 201 rigid atoms, others: [32, 2, 3, 4, 8, 9, 29, 30, 31] set([0, 1, 5, 6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 705 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113665 none O=C(CC1(C(F)(F)F)CC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 15, 15, 15, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 189, 201, 201, 201, 201, 201, 201, 45, 45, 45, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 45, 189, 189, 201, 201, 201, 201, 85, 45, 45, 45, 45, 9, 5, 5, 3, 3, 45, 45] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 748 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113665 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113665/1 /scratch/stefan/7770410/working/building/REAL300020113665 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 939) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/939 `/scratch/stefan/7770410/working/3D/939' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1(C(F)(F)F)CC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113665.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113665 none O=C(CC1(C(F)(F)F)CC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 15, 15, 15, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 22, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 11, 11, 11, 28, 43, 45, 45, 45, 45, 11, 11, 1, 22, 22, 33, 33, 33, 33, 6, 1, 1, 1, 1, 11, 28, 28, 43, 43, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 44, 10, 11, 12, 13, 14, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 289 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113665 none O=C(CC1(C(F)(F)F)CC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 15, 15, 15, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 91, 112, 112, 112, 112, 112, 112, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 91, 91, 112, 112, 112, 112, 33, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [38, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 430 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113665 none O=C(CC1(C(F)(F)F)CC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 15, 15, 15, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 1, 1, 1, 2, 2, 2, 1, 1, 15, 15, 33, 33, 33, 112, 112, 112, 169, 201, 201, 201, 201, 201, 112, 112, 33, 5, 5, 1, 1, 1, 1, 15, 33, 33, 33, 33, 112, 169, 169, 201, 201, 33, 33] 201 rigid atoms, others: [32, 2, 3, 4, 8, 9, 29, 30, 31] set([0, 1, 5, 6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 700 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113665 none O=C(CC1(C(F)(F)F)CC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 15, 15, 15, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 189, 201, 201, 201, 201, 201, 201, 46, 46, 46, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 46, 189, 189, 201, 201, 201, 201, 85, 46, 46, 46, 46, 10, 5, 5, 3, 3, 46, 46] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 748 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113665 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113665 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113665/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113665/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113665 Building REAL300020113666 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113666' /scratch/stefan/7770410/working/building/REAL300020113666 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113666 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113666/0 /scratch/stefan/7770410/working/building/REAL300020113666 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/940 `/scratch/stefan/7770410/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=C(CCOC2)N1) `REAL300020113666.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113666 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=C(CCOC2)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 12, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 7, 7, 7, 1, 1, 1, 1, 1, 8, 13, 16, 16, 16, 16, 1, 1, 7, 18, 46, 46, 46, 46, 46, 46, 46, 46, 18, 7, 7, 7, 7, 1, 8, 8, 13, 13, 7, 7, 46, 46, 46, 46, 46, 46, 46, 46] 86 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 145 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113666 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=C(CCOC2)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 12, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 46, 46, 46, 19, 19, 19, 6, 4, 1, 1, 1, 1, 1, 1, 19, 19, 46, 65, 87, 87, 87, 87, 87, 87, 87, 87, 65, 46, 46, 46, 46, 19, 6, 6, 4, 4, 46, 46, 87, 87, 87, 87, 87, 87, 87, 87] 87 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 223 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113666 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=C(CCOC2)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 12, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 28, 38, 45, 45, 45, 45, 7, 7, 1, 6, 24, 24, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 7, 28, 28, 38, 38, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24] 86 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113666 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=C(CCOC2)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 12, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 24, 24, 24, 46, 46, 46, 77, 86, 86, 86, 86, 86, 46, 46, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 24, 24, 24, 24, 46, 77, 77, 86, 86, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1] 86 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 306 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113666 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113666/1 /scratch/stefan/7770410/working/building/REAL300020113666 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 941) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/941 `/scratch/stefan/7770410/working/3D/941' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=C(CCOC2)N1) `REAL300020113666.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113666/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113666 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=C(CCOC2)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 12, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 7, 7, 7, 1, 1, 1, 1, 1, 8, 13, 16, 16, 16, 16, 1, 1, 7, 19, 47, 47, 47, 47, 47, 47, 47, 47, 19, 7, 7, 7, 7, 1, 8, 8, 13, 13, 7, 7, 47, 47, 47, 47, 47, 47, 47, 47] 87 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 147 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113666 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=C(CCOC2)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 12, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 46, 46, 46, 20, 20, 20, 6, 4, 1, 1, 1, 1, 1, 1, 20, 20, 46, 65, 87, 87, 87, 87, 87, 87, 87, 87, 65, 46, 46, 46, 46, 20, 6, 6, 4, 4, 46, 46, 87, 87, 87, 87, 87, 87, 87, 87] 87 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 223 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113666 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=C(CCOC2)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 12, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 28, 38, 45, 45, 45, 45, 7, 7, 1, 6, 24, 24, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 7, 28, 28, 38, 38, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24] 87 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113666 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=C(CCOC2)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 12, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 24, 24, 24, 47, 47, 47, 78, 87, 87, 87, 87, 87, 47, 47, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 24, 24, 24, 24, 47, 78, 78, 87, 87, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1] 87 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 308 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113666 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113666 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113666/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113666/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113666 Building REAL300020113667 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113667' /scratch/stefan/7770410/working/building/REAL300020113667 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113667 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113667/0 /scratch/stefan/7770410/working/building/REAL300020113667 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/942 `/scratch/stefan/7770410/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC(C2CC2)=NO1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113667.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113667 none O=C(CC1=CC(C2CC2)=NO1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 5, 5, 5, 8, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 20, 7, 7, 7, 1, 1, 1, 1, 7, 7, 39, 39, 57, 57, 57, 136, 136, 136, 186, 201, 201, 201, 201, 201, 136, 136, 57, 20, 20, 7, 1, 1, 1, 1, 1, 39, 57, 57, 57, 57, 136, 186, 186, 201, 201, 57, 57] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 31] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 652 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113667 none O=C(CC1=CC(C2CC2)=NO1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 5, 5, 5, 8, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 113, 120, 120, 120, 201, 201, 120, 120, 32, 32, 32, 10, 10, 10, 6, 2, 1, 1, 1, 1, 1, 1, 10, 10, 32, 113, 113, 120, 201, 201, 201, 201, 201, 43, 32, 32, 32, 32, 10, 6, 6, 2, 2, 32, 32] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 753 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113667 none O=C(CC1=CC(C2CC2)=NO1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 5, 5, 5, 8, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 15, 21, 21, 21, 57, 57, 21, 21, 1, 1, 1, 1, 1, 7, 7, 7, 18, 29, 29, 29, 29, 29, 7, 7, 1, 15, 15, 21, 57, 57, 57, 57, 57, 4, 1, 1, 1, 1, 7, 18, 18, 29, 29, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 292 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113667 none O=C(CC1=CC(C2CC2)=NO1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 5, 5, 5, 8, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 4, 1, 1, 1, 1, 1, 7, 7, 1, 1, 12, 12, 21, 21, 21, 67, 67, 67, 102, 123, 123, 123, 123, 123, 67, 67, 21, 4, 4, 1, 7, 7, 7, 7, 7, 12, 21, 21, 21, 21, 67, 102, 102, 123, 123, 21, 21] 201 rigid atoms, others: [2, 3, 4, 5, 6, 9, 10, 30] set([0, 1, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 452 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113667 none O=C(CC1=CC(C2CC2)=NO1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 5, 5, 5, 8, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 52, 67, 67, 67, 136, 136, 67, 67, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 52, 52, 67, 136, 136, 136, 136, 136, 15, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 487 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113667 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113667/1 /scratch/stefan/7770410/working/building/REAL300020113667 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 943) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/943 `/scratch/stefan/7770410/working/3D/943' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC(C2CC2)=NO1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113667.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113667 none O=C(CC1=CC(C2CC2)=NO1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 5, 5, 5, 8, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 20, 7, 7, 7, 1, 1, 1, 1, 7, 7, 38, 38, 56, 56, 56, 137, 137, 137, 185, 201, 201, 201, 201, 201, 137, 137, 56, 20, 20, 7, 1, 1, 1, 1, 1, 38, 56, 56, 56, 56, 137, 185, 185, 201, 201, 56, 56] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 31] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 644 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113667 none O=C(CC1=CC(C2CC2)=NO1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 5, 5, 5, 8, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 112, 119, 119, 119, 201, 201, 119, 119, 31, 31, 31, 9, 9, 9, 5, 2, 1, 1, 1, 1, 1, 1, 9, 9, 31, 112, 112, 119, 201, 201, 201, 201, 201, 40, 31, 31, 31, 31, 9, 5, 5, 2, 2, 31, 31] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 755 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113667 none O=C(CC1=CC(C2CC2)=NO1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 5, 5, 5, 8, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 15, 21, 21, 21, 56, 56, 21, 21, 1, 1, 1, 1, 1, 7, 7, 7, 18, 29, 29, 29, 29, 29, 7, 7, 1, 15, 15, 21, 56, 56, 56, 56, 56, 4, 1, 1, 1, 1, 7, 18, 18, 29, 29, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 290 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113667 none O=C(CC1=CC(C2CC2)=NO1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 5, 5, 5, 8, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 4, 1, 1, 1, 1, 1, 7, 7, 1, 1, 12, 12, 21, 21, 21, 67, 67, 67, 102, 124, 124, 124, 124, 124, 67, 67, 21, 4, 4, 1, 7, 7, 7, 7, 7, 12, 21, 21, 21, 21, 67, 102, 102, 124, 124, 21, 21] 201 rigid atoms, others: [2, 3, 4, 5, 6, 9, 10, 30] set([0, 1, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 458 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113667 none O=C(CC1=CC(C2CC2)=NO1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 5, 5, 5, 8, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 52, 67, 67, 67, 137, 137, 67, 67, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 52, 52, 67, 137, 137, 137, 137, 137, 15, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 493 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113667 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113667 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113667/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113667/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113667 Building REAL300020113668 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113668' /scratch/stefan/7770410/working/building/REAL300020113668 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113668 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113668/0 /scratch/stefan/7770410/working/building/REAL300020113668 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/944 `/scratch/stefan/7770410/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NC2=CC=NN21) `REAL300020113668.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113668 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NC2=CC=NN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 20, 20, 20, 20, 1, 1, 13, 52, 83, 83, 54, 83, 83, 83, 83, 83, 52, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 83, 83, 83, 83] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 318 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113668 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NC2=CC=NN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [195, 195, 107, 107, 107, 21, 21, 21, 6, 4, 1, 1, 1, 1, 1, 1, 21, 21, 107, 195, 201, 201, 201, 201, 201, 201, 201, 201, 195, 107, 107, 107, 107, 21, 6, 6, 4, 4, 107, 107, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 549 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113668 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NC2=CC=NN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 66, 88, 107, 107, 107, 107, 13, 13, 1, 6, 16, 16, 6, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 66, 66, 88, 88, 1, 1, 16, 16, 16, 16] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 423 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113668 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NC2=CC=NN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 16, 16, 16, 83, 83, 83, 177, 201, 201, 201, 201, 201, 83, 83, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 83, 177, 177, 201, 201, 16, 16, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 701 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113668 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113668/1 /scratch/stefan/7770410/working/building/REAL300020113668 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 945) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/945 `/scratch/stefan/7770410/working/3D/945' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NC2=CC=NN21) `REAL300020113668.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113668 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NC2=CC=NN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 20, 20, 20, 20, 1, 1, 13, 52, 83, 83, 54, 83, 83, 83, 83, 83, 52, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 83, 83, 83, 83] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 318 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113668 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NC2=CC=NN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [195, 195, 108, 108, 108, 21, 21, 21, 6, 4, 1, 1, 1, 1, 1, 1, 21, 21, 108, 195, 201, 201, 201, 201, 201, 201, 201, 201, 195, 108, 108, 108, 108, 21, 6, 6, 4, 4, 108, 108, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 551 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113668 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NC2=CC=NN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 66, 88, 107, 107, 107, 107, 13, 13, 1, 6, 16, 16, 6, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 66, 66, 88, 88, 1, 1, 16, 16, 16, 16] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 423 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113668 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NC2=CC=NN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 16, 16, 16, 83, 83, 83, 177, 201, 201, 201, 201, 201, 83, 83, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 83, 177, 177, 201, 201, 16, 16, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 701 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113668 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113668 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113668/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113668/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113668 Building REAL300020113669 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113669' /scratch/stefan/7770410/working/building/REAL300020113669 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113669 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113669/0 /scratch/stefan/7770410/working/building/REAL300020113669 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/946 `/scratch/stefan/7770410/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCC(=O)NC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113669.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113669 none O=C(CC1CCC(=O)NC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 1, 11, 8, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 37, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 1, 6, 6, 6, 8, 11, 11, 11, 11, 11, 6, 6, 1, 37, 37, 54, 54, 54, 54, 54, 54, 54, 54, 6, 1, 1, 1, 1, 6, 8, 8, 11, 11, 1, 1] 63 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 217 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113669 none O=C(CC1CCC(=O)NC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 1, 11, 8, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 50, 61, 61, 61, 61, 61, 61, 6, 6, 6, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 1, 1, 6, 50, 50, 61, 61, 61, 61, 61, 61, 61, 61, 16, 6, 6, 6, 6, 1, 3, 3, 5, 5, 6, 6] 63 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 237 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113669 none O=C(CC1CCC(=O)NC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 1, 11, 8, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [26, 8, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 54, 54, 54, 61, 61, 61, 62, 63, 63, 63, 63, 63, 61, 61, 54, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 26, 54, 54, 54, 54, 61, 62, 62, 63, 63, 54, 54] 63 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 36, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113669 none O=C(CC1CCC(=O)NC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 1, 11, 8, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 52, 61, 61, 61, 61, 61, 61, 11, 11, 11, 6, 6, 6, 5, 2, 1, 1, 1, 1, 1, 1, 6, 6, 11, 52, 52, 61, 61, 61, 61, 61, 61, 61, 61, 20, 11, 11, 11, 11, 6, 5, 5, 2, 2, 11, 11] 61 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 230 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113669 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113669/1 /scratch/stefan/7770410/working/building/REAL300020113669 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 947) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/947 `/scratch/stefan/7770410/working/3D/947' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCC(=O)NC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113669.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113669 none O=C(CC1CCC(=O)NC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 1, 11, 8, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 37, 55, 55, 55, 55, 55, 55, 1, 1, 1, 1, 1, 6, 6, 6, 8, 10, 10, 10, 10, 10, 6, 6, 1, 37, 37, 55, 55, 55, 55, 55, 55, 55, 55, 6, 1, 1, 1, 1, 6, 8, 8, 10, 10, 1, 1] 63 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 215 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113669 none O=C(CC1CCC(=O)NC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 1, 11, 8, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 51, 62, 62, 62, 62, 62, 62, 6, 6, 6, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 1, 1, 6, 51, 51, 62, 62, 62, 62, 62, 62, 62, 62, 16, 6, 6, 6, 6, 1, 3, 3, 4, 4, 6, 6] 63 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 234 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113669 none O=C(CC1CCC(=O)NC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 1, 11, 8, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [27, 8, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 55, 55, 55, 62, 62, 62, 62, 63, 63, 63, 63, 63, 62, 62, 55, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 27, 55, 55, 55, 55, 62, 62, 62, 63, 63, 55, 55] 63 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 36, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113669 none O=C(CC1CCC(=O)NC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 1, 11, 8, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 51, 60, 60, 60, 60, 60, 60, 10, 10, 10, 5, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 5, 5, 10, 51, 51, 60, 60, 60, 60, 60, 60, 60, 60, 19, 10, 10, 10, 10, 5, 5, 5, 2, 2, 10, 10] 60 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 228 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113669 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113669 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113669/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113669/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113669 Building REAL300020113670 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113670' /scratch/stefan/7770410/working/building/REAL300020113670 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113670 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113670/0 /scratch/stefan/7770410/working/building/REAL300020113670 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/948 `/scratch/stefan/7770410/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CC2CCC1O2)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113670.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113670 none O=C(CC1CC2CCC1O2)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 25, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 8, 8, 8, 24, 37, 39, 39, 39, 39, 8, 8, 1, 25, 25, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 1, 1, 1, 1, 8, 24, 24, 37, 37, 1, 1] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 294 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113670 none O=C(CC1CC2CCC1O2)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 93, 120, 120, 120, 120, 120, 120, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 8, 93, 93, 120, 120, 120, 120, 120, 120, 120, 120, 120, 21, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 458 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113670 none O=C(CC1CC2CCC1O2)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 39, 39, 39, 120, 120, 120, 169, 201, 201, 201, 201, 201, 120, 120, 39, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 39, 39, 39, 39, 120, 169, 169, 201, 201, 39, 39] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 37, 35, 36, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 687 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113670 none O=C(CC1CC2CCC1O2)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 187, 201, 201, 201, 201, 201, 201, 40, 40, 40, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 40, 187, 187, 201, 201, 201, 201, 201, 201, 201, 201, 201, 68, 40, 40, 40, 40, 10, 6, 6, 4, 4, 40, 40] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 761 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113670 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113670/1 /scratch/stefan/7770410/working/building/REAL300020113670 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 949) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/949 `/scratch/stefan/7770410/working/3D/949' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CC2CCC1O2)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113670.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113670/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113670 none O=C(CC1CC2CCC1O2)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 25, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 8, 8, 8, 24, 37, 39, 39, 39, 39, 8, 8, 1, 25, 25, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 1, 1, 1, 1, 8, 24, 24, 37, 37, 1, 1] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 294 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113670 none O=C(CC1CC2CCC1O2)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 93, 120, 120, 120, 120, 120, 120, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 8, 93, 93, 120, 120, 120, 120, 120, 120, 120, 120, 120, 21, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 458 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113670 none O=C(CC1CC2CCC1O2)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 39, 39, 39, 120, 120, 120, 169, 201, 201, 201, 201, 201, 120, 120, 39, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 39, 39, 39, 39, 120, 169, 169, 201, 201, 39, 39] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 37, 35, 36, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 687 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113670 none O=C(CC1CC2CCC1O2)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 187, 201, 201, 201, 201, 201, 201, 41, 41, 41, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 41, 187, 187, 201, 201, 201, 201, 201, 201, 201, 201, 201, 69, 41, 41, 41, 41, 12, 6, 6, 4, 4, 41, 41] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 757 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113670 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113670 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113670/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113670/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113670 Building REAL300020113671 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113671' /scratch/stefan/7770410/working/building/REAL300020113671 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113671 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113671/0 /scratch/stefan/7770410/working/building/REAL300020113671 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/950 `/scratch/stefan/7770410/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=NC(C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113671.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113671 none CCN1N=NC(C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [29, 21, 21, 21, 21, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 11, 6, 6, 1, 29, 29, 29, 29, 29, 21, 21, 21, 6, 1, 1, 1, 1, 6, 11, 11, 11, 11, 1, 1] 43 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 114 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113671 none CCN1N=NC(C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [41, 32, 32, 32, 32, 32, 32, 18, 18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 6, 41, 41, 41, 41, 41, 32, 32, 32, 18, 6, 6, 6, 6, 1, 4, 4, 4, 4, 6, 6] 43 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 135 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113671 none CCN1N=NC(C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 21, 21, 21, 32, 32, 32, 34, 34, 34, 34, 34, 34, 32, 32, 21, 5, 5, 5, 5, 5, 2, 2, 2, 8, 21, 21, 21, 21, 32, 34, 34, 34, 34, 21, 21] 43 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 107 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113671 none CCN1N=NC(C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 33, 33, 33, 33, 33, 33, 21, 21, 21, 12, 12, 12, 4, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 4, 4, 12, 41, 41, 41, 41, 41, 33, 33, 33, 21, 12, 12, 12, 12, 4, 4, 4, 2, 2, 12, 12] 41 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 133 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113671 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113671/1 /scratch/stefan/7770410/working/building/REAL300020113671 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 951) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/951 `/scratch/stefan/7770410/working/3D/951' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=NC(C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113671.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113671/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113671 none CCN1N=NC(C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [29, 21, 21, 21, 21, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 11, 6, 6, 1, 29, 29, 29, 29, 29, 21, 21, 21, 6, 1, 1, 1, 1, 6, 11, 11, 11, 11, 1, 1] 42 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 114 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113671 none CCN1N=NC(C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [41, 32, 32, 32, 32, 32, 32, 18, 18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 6, 41, 41, 41, 41, 41, 32, 32, 32, 18, 6, 6, 6, 6, 1, 4, 4, 4, 4, 6, 6] 42 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 135 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113671 none CCN1N=NC(C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 21, 21, 21, 32, 32, 32, 34, 34, 34, 34, 34, 34, 32, 32, 21, 5, 5, 5, 5, 5, 2, 2, 2, 8, 21, 21, 21, 21, 32, 34, 34, 34, 34, 21, 21] 42 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 107 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113671 none CCN1N=NC(C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 33, 33, 33, 33, 33, 33, 21, 21, 21, 12, 12, 12, 4, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 4, 4, 12, 40, 40, 40, 40, 40, 33, 33, 33, 21, 12, 12, 12, 12, 4, 4, 4, 2, 2, 12, 12] 40 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 127 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113671 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113671 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113671/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113671/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113671 Building REAL300020113672 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113672' /scratch/stefan/7770410/working/building/REAL300020113672 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113672 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113672/0 /scratch/stefan/7770410/working/building/REAL300020113672 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/952 `/scratch/stefan/7770410/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NOC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113672.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113672 none CC(C)C1=NOC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 45, 62, 74, 74, 74, 74, 12, 12, 1, 26, 26, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 12, 45, 45, 62, 62, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 301 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113672 none CC(C)C1=NOC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 111, 111, 111, 111, 111, 40, 40, 40, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 12, 111, 111, 111, 111, 111, 111, 111, 111, 40, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 239 number of broken/clashed sets: 28 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113672 none CC(C)C1=NOC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 26, 26, 26, 111, 111, 111, 169, 201, 201, 201, 201, 201, 111, 111, 26, 2, 2, 2, 1, 1, 1, 1, 1, 11, 26, 26, 26, 26, 111, 169, 169, 201, 201, 26, 26] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 7, 34, 5, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 670 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113672 none CC(C)C1=NOC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 144, 144, 144, 74, 74, 74, 16, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 74, 201, 201, 201, 201, 201, 201, 201, 201, 144, 74, 74, 74, 74, 16, 6, 6, 4, 4, 74, 74] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 488 number of broken/clashed sets: 28 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113672 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113672/1 /scratch/stefan/7770410/working/building/REAL300020113672 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 953) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/953 `/scratch/stefan/7770410/working/3D/953' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NOC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113672.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113672 none CC(C)C1=NOC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 43, 60, 72, 72, 72, 72, 12, 12, 1, 26, 26, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 12, 43, 43, 60, 60, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 295 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113672 none CC(C)C1=NOC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 113, 113, 113, 113, 40, 40, 40, 12, 12, 12, 1, 1, 1, 1, 1, 8, 10, 14, 14, 14, 14, 1, 1, 12, 113, 113, 113, 113, 113, 113, 113, 113, 40, 12, 12, 12, 12, 1, 8, 8, 10, 10, 12, 12] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 240 number of broken/clashed sets: 28 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113672 none CC(C)C1=NOC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 26, 26, 26, 113, 113, 113, 169, 201, 201, 201, 201, 201, 113, 113, 26, 2, 2, 2, 1, 1, 1, 1, 1, 11, 26, 26, 26, 26, 113, 169, 169, 201, 201, 26, 26] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 7, 34, 5, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 665 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113672 none CC(C)C1=NOC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 144, 144, 144, 73, 73, 73, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 73, 201, 201, 201, 201, 201, 201, 201, 201, 144, 73, 73, 73, 73, 15, 6, 6, 4, 4, 73, 73] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 490 number of broken/clashed sets: 28 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113672 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113672 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113672/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113672/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113672 Building REAL300020113673 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113673' /scratch/stefan/7770410/working/building/REAL300020113673 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113673 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113673/0 /scratch/stefan/7770410/working/building/REAL300020113673 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/954 `/scratch/stefan/7770410/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCNC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113673.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113673 none O=C(CC1CCNC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 20, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 9, 9, 9, 27, 41, 43, 43, 43, 43, 9, 9, 1, 20, 20, 27, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 9, 27, 27, 41, 41, 1, 1] 201 rigid atoms, others: [45, 35, 36, 37, 38, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 271 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113673 none O=C(CC1CCNC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 86, 102, 102, 102, 102, 102, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 86, 86, 102, 102, 102, 102, 102, 102, 28, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 391 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113673 none O=C(CC1CCNC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 27, 27, 27, 102, 102, 102, 168, 201, 201, 201, 201, 201, 102, 102, 27, 6, 6, 1, 1, 1, 1, 1, 1, 12, 27, 27, 27, 27, 102, 168, 168, 201, 201, 27, 27] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 722 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113673 none O=C(CC1CCNC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 177, 201, 201, 201, 201, 201, 43, 43, 43, 11, 11, 11, 5, 3, 1, 1, 1, 1, 1, 1, 11, 11, 43, 177, 177, 201, 201, 201, 201, 201, 201, 84, 43, 43, 43, 43, 11, 5, 5, 3, 3, 43, 43] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 754 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113673 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113673/1 /scratch/stefan/7770410/working/building/REAL300020113673 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 955) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/955 `/scratch/stefan/7770410/working/3D/955' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCNC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113673.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113673 none O=C(CC1CCNC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 20, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 9, 9, 9, 27, 41, 43, 43, 43, 43, 9, 9, 1, 20, 20, 27, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 9, 27, 27, 41, 41, 1, 1] 201 rigid atoms, others: [45, 35, 36, 37, 38, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 271 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113673 none O=C(CC1CCNC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 86, 102, 102, 102, 102, 102, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 86, 86, 102, 102, 102, 102, 102, 102, 28, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 391 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113673 none O=C(CC1CCNC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 27, 27, 27, 102, 102, 102, 168, 201, 201, 201, 201, 201, 102, 102, 27, 6, 6, 1, 1, 1, 1, 1, 1, 12, 27, 27, 27, 27, 102, 168, 168, 201, 201, 27, 27] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 722 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113673 none O=C(CC1CCNC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 177, 201, 201, 201, 201, 201, 43, 43, 43, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 43, 177, 177, 201, 201, 201, 201, 201, 201, 84, 43, 43, 43, 43, 11, 6, 6, 4, 4, 43, 43] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 755 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113673 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113673 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113673/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113673/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113673 Building REAL300020113674 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113674' /scratch/stefan/7770410/working/building/REAL300020113674 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113674 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113674/0 /scratch/stefan/7770410/working/building/REAL300020113674 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/956 `/scratch/stefan/7770410/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1) `REAL300020113674.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113674 none CC1=NC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 40, 21, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 24, 36, 36, 36, 36, 36, 8, 8, 1, 40, 40, 40, 40, 40, 21, 21, 5, 1, 1, 1, 1, 8, 24, 24, 36, 36, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 242 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113674 none CC1=NC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 116, 116, 83, 19, 19, 19, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 116, 116, 116, 116, 116, 83, 83, 19, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 377 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113674 none CC1=NC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 23, 23, 23, 40, 40, 40, 116, 116, 116, 173, 201, 201, 201, 201, 201, 116, 116, 40, 1, 2, 2, 2, 1, 6, 6, 23, 40, 40, 40, 40, 116, 173, 173, 201, 201, 40, 40] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 683 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113674 none CC1=NC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 193, 63, 63, 63, 37, 37, 37, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 37, 201, 201, 201, 201, 201, 193, 193, 63, 37, 37, 37, 37, 9, 5, 5, 3, 3, 37, 37] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 719 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113674 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113674/1 /scratch/stefan/7770410/working/building/REAL300020113674 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 957) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/957 `/scratch/stefan/7770410/working/3D/957' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1) `REAL300020113674.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113674/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113674 none CC1=NC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 40, 21, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 24, 36, 36, 36, 36, 36, 8, 8, 1, 40, 40, 40, 40, 40, 21, 21, 5, 1, 1, 1, 1, 8, 24, 24, 36, 36, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 242 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113674 none CC1=NC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 116, 116, 83, 19, 19, 19, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 116, 116, 116, 116, 116, 83, 83, 19, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 377 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113674 none CC1=NC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 23, 23, 23, 40, 40, 40, 116, 116, 116, 173, 201, 201, 201, 201, 201, 116, 116, 40, 1, 2, 2, 2, 1, 6, 6, 23, 40, 40, 40, 40, 116, 173, 173, 201, 201, 40, 40] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 683 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113674 none CC1=NC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 193, 63, 63, 63, 37, 37, 37, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 37, 201, 201, 201, 201, 201, 193, 193, 63, 37, 37, 37, 37, 9, 5, 5, 3, 3, 37, 37] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 719 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113674 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113674 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113674/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113674/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113674 Building REAL300020113675 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113675' /scratch/stefan/7770410/working/building/REAL300020113675 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for REAL300020113675 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113675/0 /scratch/stefan/7770410/working/building/REAL300020113675 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/958 `/scratch/stefan/7770410/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[N@@H+]1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1) `REAL300020113675.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113675 none CC(C)C[N@@H+]1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 14, 14, 14, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 10, 10, 10, 10, 10, 10, 9, 9, 1, 14, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 9, 10, 10, 10, 10, 1, 1, 14, 14] 51 rigid atoms, others: [47, 15, 12, 11, 44, 13, 14, 45, 46, 54, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50, 51, 52, 55, 56]) total number of confs: 58 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113675 none CC(C)C[N@@H+]1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 9, 9, 9, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 9, 9, 9, 9, 1, 3, 3, 3, 3, 9, 9, 50, 50] 51 rigid atoms, others: [48, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 156 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113675 none CC(C)C[N@@H+]1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 14, 14, 14, 50, 50, 50, 51, 51, 51, 51, 51, 51, 50, 50, 14, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 7, 14, 14, 14, 14, 50, 51, 51, 51, 51, 14, 14, 1, 1] 51 rigid atoms, others: [3, 4, 5, 6, 7, 8, 41, 42, 39, 40, 9, 56, 55, 38, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 97 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113675 none CC(C)C[N@@H+]1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 51, 51, 51, 51, 51, 26, 26, 26, 10, 10, 10, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 26, 10, 10, 10, 10, 3, 3, 3, 1, 1, 10, 10, 51, 51] 51 rigid atoms, others: [19, 18, 51, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 53, 54, 55, 56]) total number of confs: 156 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113675 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113675/1 /scratch/stefan/7770410/working/building/REAL300020113675 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 959) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/959 `/scratch/stefan/7770410/working/3D/959' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[N@H+]1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1) `REAL300020113675.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113675/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113675 none CC(C)C[N@H+]1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 20, 20, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 25, 25, 25, 25, 25, 25, 12, 12, 1, 20, 24, 24, 24, 24, 24, 24, 24, 24, 24, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 12, 25, 25, 25, 25, 1, 1, 20, 20] 88 rigid atoms, others: [47, 15, 12, 11, 44, 13, 14, 45, 46, 54, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50, 51, 52, 55, 56]) total number of confs: 159 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113675 none CC(C)C[N@H+]1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 71, 71, 71, 71, 71, 35, 35, 35, 12, 12, 12, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 12, 71, 73, 73, 73, 73, 73, 73, 73, 73, 73, 71, 71, 71, 71, 71, 35, 12, 12, 12, 12, 1, 5, 5, 5, 5, 12, 12, 71, 71] 88 rigid atoms, others: [48, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 238 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113675 none CC(C)C[N@H+]1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 20, 20, 20, 71, 71, 71, 88, 88, 88, 88, 88, 88, 71, 71, 20, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 8, 20, 20, 20, 20, 71, 88, 88, 88, 88, 20, 20, 1, 1] 88 rigid atoms, others: [3, 4, 5, 6, 7, 8, 41, 42, 39, 40, 9, 56, 55, 38, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 226 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113675 none CC(C)C[N@H+]1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 88, 88, 88, 88, 88, 57, 57, 57, 25, 25, 25, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 25, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 57, 25, 25, 25, 25, 5, 3, 3, 1, 1, 25, 25, 88, 88] 88 rigid atoms, others: [19, 18, 51, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 53, 54, 55, 56]) total number of confs: 266 number of broken/clashed sets: 6 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113675 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `2' /scratch/stefan/7770410/working/building/REAL300020113675/2 /scratch/stefan/7770410/working/building/REAL300020113675 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 2 (index: 960) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/960 `/scratch/stefan/7770410/working/3D/960' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[N@@H+]1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1) `REAL300020113675.mol2' -> `2.mol2' `temp.mol2' -> `REAL300020113675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113675/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113675 none CC(C)C[N@@H+]1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 14, 14, 14, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 10, 10, 10, 10, 10, 10, 9, 9, 1, 14, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 9, 10, 10, 10, 10, 1, 1, 14, 14] 51 rigid atoms, others: [47, 15, 12, 11, 44, 13, 14, 45, 46, 54, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50, 51, 52, 55, 56]) total number of confs: 58 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113675 none CC(C)C[N@@H+]1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 9, 9, 9, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 9, 9, 9, 9, 1, 3, 3, 3, 3, 9, 9, 50, 50] 51 rigid atoms, others: [48, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 156 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113675 none CC(C)C[N@@H+]1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 14, 14, 14, 50, 50, 50, 51, 51, 51, 51, 51, 51, 50, 50, 14, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 7, 14, 14, 14, 14, 50, 51, 51, 51, 51, 14, 14, 1, 1] 51 rigid atoms, others: [3, 4, 5, 6, 7, 8, 41, 42, 39, 40, 9, 56, 55, 38, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 97 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113675 none CC(C)C[N@@H+]1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 51, 51, 51, 51, 51, 26, 26, 26, 10, 10, 10, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 26, 10, 10, 10, 10, 3, 3, 3, 1, 1, 10, 10, 51, 51] 51 rigid atoms, others: [19, 18, 51, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 53, 54, 55, 56]) total number of confs: 156 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113675 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `3' /scratch/stefan/7770410/working/building/REAL300020113675/3 /scratch/stefan/7770410/working/building/REAL300020113675 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 3 (index: 961) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/961 `/scratch/stefan/7770410/working/3D/961' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[N@H+]1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1) `REAL300020113675.mol2' -> `3.mol2' `temp.mol2' -> `REAL300020113675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113675/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113675 none CC(C)C[N@H+]1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 21, 21, 21, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 25, 25, 25, 25, 25, 25, 12, 12, 1, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 12, 25, 25, 25, 25, 1, 1, 21, 21] 88 rigid atoms, others: [47, 15, 12, 11, 44, 13, 14, 45, 46, 54, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50, 51, 52, 55, 56]) total number of confs: 161 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113675 none CC(C)C[N@H+]1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 71, 71, 71, 71, 71, 35, 35, 35, 12, 12, 12, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 12, 71, 73, 73, 73, 73, 73, 73, 73, 73, 73, 71, 71, 71, 71, 71, 35, 12, 12, 12, 12, 1, 5, 5, 5, 5, 12, 12, 71, 71] 88 rigid atoms, others: [48, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 238 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113675 none CC(C)C[N@H+]1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 21, 21, 21, 71, 71, 71, 88, 88, 88, 88, 88, 88, 71, 71, 21, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 9, 21, 21, 21, 21, 71, 88, 88, 88, 88, 21, 21, 1, 1] 88 rigid atoms, others: [3, 4, 5, 6, 7, 8, 41, 42, 39, 40, 9, 56, 55, 38, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 226 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113675 none CC(C)C[N@H+]1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 88, 88, 88, 88, 88, 56, 56, 56, 25, 25, 25, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 25, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 56, 25, 25, 25, 25, 5, 3, 3, 1, 1, 25, 25, 88, 88] 88 rigid atoms, others: [19, 18, 51, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 53, 54, 55, 56]) total number of confs: 264 number of broken/clashed sets: 6 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113675 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113675 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 2: /scratch/stefan/7770410/working/building/REAL300020113675/2.* 1: /scratch/stefan/7770410/working/building/REAL300020113675/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113675/0.* 3: /scratch/stefan/7770410/working/building/REAL300020113675/3.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113675 Building REAL300020113676 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113676' /scratch/stefan/7770410/working/building/REAL300020113676 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113676 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113676/0 /scratch/stefan/7770410/working/building/REAL300020113676 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/962 `/scratch/stefan/7770410/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(C)C) `REAL300020113676.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113676 none CCOC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 121, 108, 87, 33, 33, 33, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 11, 11, 11, 11, 1, 1, 9, 108, 134, 134, 133, 133, 133, 133, 133, 108, 87, 87, 33, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 134, 134, 134, 134, 134, 134, 134] 201 rigid atoms, others: [40, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 730 number of broken/clashed sets: 34 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113676 none CCOC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [195, 194, 173, 145, 86, 86, 86, 38, 38, 38, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 10, 10, 38, 173, 193, 193, 195, 195, 195, 195, 195, 173, 145, 145, 86, 38, 38, 38, 38, 10, 4, 4, 4, 4, 38, 38, 193, 193, 193, 193, 193, 193, 193] 195 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 839 number of broken/clashed sets: 75 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113676 none CCOC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 38, 30, 20, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 31, 34, 41, 41, 41, 41, 9, 9, 1, 30, 50, 50, 45, 45, 45, 45, 45, 30, 20, 20, 6, 1, 1, 1, 1, 9, 31, 31, 34, 34, 1, 1, 50, 50, 50, 50, 50, 50, 50] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 45, 46, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 424 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113676 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113676/1 /scratch/stefan/7770410/working/building/REAL300020113676 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 963) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/963 `/scratch/stefan/7770410/working/3D/963' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(C)C) `REAL300020113676.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113676/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113676 none CCOC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [132, 122, 108, 87, 33, 33, 33, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 11, 11, 11, 11, 1, 1, 9, 108, 135, 135, 132, 132, 132, 132, 132, 108, 87, 87, 33, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 135, 135, 135, 135, 135, 135, 135] 201 rigid atoms, others: [40, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 726 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113676 none CCOC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [194, 193, 172, 145, 87, 87, 87, 39, 39, 39, 11, 11, 11, 4, 4, 1, 1, 1, 1, 1, 1, 11, 11, 39, 172, 192, 192, 194, 194, 194, 194, 194, 172, 145, 145, 87, 39, 39, 39, 39, 11, 4, 4, 4, 4, 39, 39, 192, 192, 192, 192, 192, 192, 192] 194 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 831 number of broken/clashed sets: 75 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113676 none CCOC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 38, 30, 20, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 30, 33, 41, 41, 41, 41, 9, 9, 1, 30, 50, 50, 44, 44, 44, 44, 44, 30, 20, 20, 6, 1, 1, 1, 1, 9, 30, 30, 33, 33, 1, 1, 50, 50, 50, 50, 50, 50, 50] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 45, 46, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 414 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113676 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113676 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113676/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113676/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113676 Building REAL300020113677 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113677' /scratch/stefan/7770410/working/building/REAL300020113677 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113677 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113677/0 /scratch/stefan/7770410/working/building/REAL300020113677 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/964 `/scratch/stefan/7770410/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCCS1(=O)=O) `REAL300020113677.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113677 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCCS1(=O)=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 14, 11, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 13, 58, 113, 113, 113, 113, 113, 113, 113, 58, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13, 113, 113, 113, 113, 113, 113, 113, 113, 113] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 375 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113677 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCCS1(=O)=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 14, 11, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [171, 171, 69, 69, 69, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 69, 171, 201, 201, 201, 201, 201, 201, 201, 171, 69, 69, 69, 69, 13, 6, 6, 4, 4, 69, 69, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 584 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113677 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCCS1(=O)=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 14, 11, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 42, 60, 69, 69, 69, 69, 13, 13, 1, 6, 27, 27, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 13, 42, 42, 60, 60, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 321 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113677 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCCS1(=O)=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 14, 11, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 27, 27, 27, 113, 113, 113, 175, 201, 201, 201, 201, 201, 113, 113, 27, 1, 1, 1, 1, 1, 1, 1, 1, 10, 27, 27, 27, 27, 113, 175, 175, 201, 201, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 39, 40, 41, 42, 43, 44, 45, 46, 47, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 655 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113677 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113677/1 /scratch/stefan/7770410/working/building/REAL300020113677 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 965) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/965 `/scratch/stefan/7770410/working/3D/965' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCCS1(=O)=O) `REAL300020113677.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113677/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113677 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCCS1(=O)=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 14, 11, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 13, 58, 113, 113, 113, 113, 113, 113, 113, 58, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13, 113, 113, 113, 113, 113, 113, 113, 113, 113] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 375 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113677 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCCS1(=O)=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 14, 11, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [172, 172, 69, 69, 69, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 69, 172, 201, 201, 201, 201, 201, 201, 201, 172, 69, 69, 69, 69, 13, 6, 6, 4, 4, 69, 69, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 580 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113677 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCCS1(=O)=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 14, 11, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 41, 59, 69, 69, 69, 69, 13, 13, 1, 6, 27, 27, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 13, 41, 41, 59, 59, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 320 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113677 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCCS1(=O)=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 14, 11, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 27, 27, 27, 113, 113, 113, 173, 201, 201, 201, 201, 201, 113, 113, 27, 1, 1, 1, 1, 1, 1, 1, 1, 10, 27, 27, 27, 27, 113, 173, 173, 201, 201, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 39, 40, 41, 42, 43, 44, 45, 46, 47, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 658 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113677 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113677 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113677/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113677/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113677 Building REAL300020113678 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113678' /scratch/stefan/7770410/working/building/REAL300020113678 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113678 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113678/0 /scratch/stefan/7770410/working/building/REAL300020113678 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/966 `/scratch/stefan/7770410/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1C=C(C2CC2)N=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113678.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113678 none O=C(CN1C=C(C2CC2)N=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 5, 5, 5, 8, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 14, 8, 8, 8, 1, 1, 1, 1, 8, 8, 28, 28, 56, 56, 56, 126, 126, 126, 179, 201, 201, 201, 201, 201, 126, 126, 56, 14, 14, 8, 1, 1, 1, 1, 1, 28, 56, 56, 56, 56, 126, 179, 179, 201, 201, 56, 56] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 31] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 692 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113678 none O=C(CN1C=C(C2CC2)N=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 5, 5, 5, 8, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 127, 127, 127, 127, 201, 201, 127, 127, 31, 31, 31, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 31, 127, 127, 127, 201, 201, 201, 201, 201, 50, 31, 31, 31, 31, 7, 4, 4, 2, 2, 31, 31] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 777 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113678 none O=C(CN1C=C(C2CC2)N=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 5, 5, 5, 8, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 18, 18, 18, 18, 56, 56, 18, 18, 1, 1, 1, 1, 1, 8, 8, 8, 21, 32, 32, 32, 32, 32, 8, 8, 1, 18, 18, 18, 56, 56, 56, 56, 56, 5, 1, 1, 1, 1, 8, 21, 21, 32, 32, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 299 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113678 none O=C(CN1C=C(C2CC2)N=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 5, 5, 5, 8, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 18, 18, 18, 58, 58, 58, 103, 125, 125, 125, 125, 125, 58, 58, 18, 3, 3, 1, 8, 8, 8, 8, 8, 7, 18, 18, 18, 18, 58, 103, 103, 125, 125, 18, 18] 201 rigid atoms, others: [2, 3, 4, 5, 6, 9, 10, 30] set([0, 1, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 479 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113678 none O=C(CN1C=C(C2CC2)N=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 5, 5, 5, 8, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 58, 58, 58, 58, 126, 126, 58, 58, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 58, 58, 58, 126, 126, 126, 126, 126, 21, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 458 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113678 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113678/1 /scratch/stefan/7770410/working/building/REAL300020113678 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 967) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/967 `/scratch/stefan/7770410/working/3D/967' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1C=C(C2CC2)N=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113678.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113678/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113678 none O=C(CN1C=C(C2CC2)N=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 5, 5, 5, 8, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 14, 8, 8, 8, 1, 1, 1, 1, 8, 8, 28, 28, 56, 56, 56, 127, 127, 127, 179, 201, 201, 201, 201, 201, 127, 127, 56, 14, 14, 8, 1, 1, 1, 1, 1, 28, 56, 56, 56, 56, 127, 179, 179, 201, 201, 56, 56] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 31] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 688 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113678 none O=C(CN1C=C(C2CC2)N=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 5, 5, 5, 8, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 127, 127, 127, 127, 201, 201, 127, 127, 32, 32, 32, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 32, 127, 127, 127, 201, 201, 201, 201, 201, 50, 32, 32, 32, 32, 8, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 774 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113678 none O=C(CN1C=C(C2CC2)N=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 5, 5, 5, 8, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 18, 18, 18, 18, 56, 56, 18, 18, 1, 1, 1, 1, 1, 8, 8, 8, 21, 32, 32, 32, 32, 32, 8, 8, 1, 18, 18, 18, 56, 56, 56, 56, 56, 5, 1, 1, 1, 1, 8, 21, 21, 32, 32, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 299 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113678 none O=C(CN1C=C(C2CC2)N=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 5, 5, 5, 8, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 18, 18, 18, 58, 58, 58, 103, 125, 125, 125, 125, 125, 58, 58, 18, 3, 3, 1, 8, 8, 8, 8, 8, 7, 18, 18, 18, 18, 58, 103, 103, 125, 125, 18, 18] 201 rigid atoms, others: [2, 3, 4, 5, 6, 9, 10, 30] set([0, 1, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 482 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113678 none O=C(CN1C=C(C2CC2)N=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 5, 5, 5, 8, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 58, 58, 58, 58, 127, 127, 58, 58, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 58, 58, 58, 127, 127, 127, 127, 127, 21, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 462 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113678 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113678 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113678/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113678/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113678 Building REAL300020113679 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113679' /scratch/stefan/7770410/working/building/REAL300020113679 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300020113679 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113679/0 /scratch/stefan/7770410/working/building/REAL300020113679 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/968 `/scratch/stefan/7770410/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)C1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC1) `REAL300020113679.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113679 none C[NH+](C)C1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 4, 4, 4, 4, 4, 4] 17 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50]) total number of confs: 17 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113679 none C[NH+](C)C1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8, 1, 3, 3, 3, 3, 8, 8, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [38, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 56 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113679 none C[NH+](C)C1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 1, 1, 3, 3, 3, 4, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 17, 17, 17, 17, 17, 4, 4, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [1, 4, 5, 45, 46, 47, 48, 49, 50, 24, 25, 26] set([0, 2, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 36 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113679 none C[NH+](C)C1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 9, 9, 9, 5, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 5, 5, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 9, 9, 5, 5, 5, 2, 2, 9, 9, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 64 number of broken/clashed sets: 5 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113679 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113679 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 0: /scratch/stefan/7770410/working/building/REAL300020113679/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113679 Building REAL300020113680 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113680' /scratch/stefan/7770410/working/building/REAL300020113680 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300020113680 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113680/0 /scratch/stefan/7770410/working/building/REAL300020113680 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/969 `/scratch/stefan/7770410/working/3D/969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(CN1C=CC=N1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113680.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113680 none CN(C)C(CN1C=CC=N1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 22, 32, 6, 22, 34, 58, 58, 58, 58, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 29, 33, 44, 44, 44, 44, 6, 6, 1, 32, 32, 32, 32, 32, 32, 22, 34, 34, 58, 58, 58, 6, 1, 1, 1, 1, 6, 29, 29, 33, 33, 1, 1] 201 rigid atoms, others: [45, 44, 42, 43, 12, 13, 14, 15, 16, 51, 52, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50]) total number of confs: 346 number of broken/clashed sets: 36 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113680 none CN(C)C(CN1C=CC=N1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 64, 74, 21, 64, 82, 118, 118, 118, 118, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 9, 11, 17, 17, 17, 17, 1, 1, 6, 74, 74, 74, 74, 74, 74, 64, 82, 82, 118, 118, 118, 21, 6, 6, 6, 6, 1, 9, 9, 11, 11, 6, 6] 201 rigid atoms, others: [46, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 478 number of broken/clashed sets: 36 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113680 none CN(C)C(CN1C=CC=N1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 13, 29, 7, 1, 1, 1, 1, 1, 1, 13, 29, 29, 29, 58, 58, 58, 118, 118, 118, 195, 198, 201, 201, 201, 201, 118, 118, 58, 29, 29, 29, 29, 29, 29, 13, 7, 7, 1, 1, 1, 29, 58, 58, 58, 58, 118, 195, 195, 198, 198, 58, 58] 201 rigid atoms, others: [4, 5, 38, 7, 8, 9, 39, 40, 6] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 733 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113680 none CN(C)C(CN1C=CC=N1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [190, 185, 190, 116, 185, 190, 201, 201, 201, 201, 116, 116, 56, 56, 56, 25, 25, 25, 6, 4, 1, 1, 1, 1, 1, 1, 25, 25, 56, 190, 190, 190, 190, 190, 190, 185, 190, 190, 201, 201, 201, 116, 56, 56, 56, 56, 25, 6, 6, 4, 4, 56, 56] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 746 number of broken/clashed sets: 36 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113680 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113680/1 /scratch/stefan/7770410/working/building/REAL300020113680 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 970) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/970 `/scratch/stefan/7770410/working/3D/970' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(CN1C=CC=N1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113680.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113680/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113680 none CN(C)C(CN1C=CC=N1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 22, 33, 6, 22, 34, 57, 57, 57, 57, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 29, 33, 45, 45, 45, 45, 6, 6, 1, 33, 33, 33, 33, 33, 33, 22, 34, 34, 57, 57, 57, 6, 1, 1, 1, 1, 6, 29, 29, 33, 33, 1, 1] 201 rigid atoms, others: [45, 44, 42, 43, 12, 13, 14, 15, 16, 51, 52, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50]) total number of confs: 350 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113680 none CN(C)C(CN1C=CC=N1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 64, 75, 21, 64, 82, 117, 117, 117, 117, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 9, 11, 17, 17, 17, 17, 1, 1, 6, 75, 75, 75, 75, 75, 75, 64, 82, 82, 117, 117, 117, 21, 6, 6, 6, 6, 1, 9, 9, 11, 11, 6, 6] 201 rigid atoms, others: [46, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 480 number of broken/clashed sets: 35 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113680 none CN(C)C(CN1C=CC=N1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 12, 29, 7, 1, 1, 1, 1, 1, 1, 12, 28, 28, 28, 57, 57, 57, 117, 117, 117, 195, 198, 201, 201, 201, 201, 117, 117, 57, 29, 29, 29, 29, 29, 29, 12, 7, 7, 1, 1, 1, 28, 57, 57, 57, 57, 117, 195, 195, 198, 198, 57, 57] 201 rigid atoms, others: [4, 5, 38, 7, 8, 9, 39, 40, 6] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 735 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113680 none CN(C)C(CN1C=CC=N1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [190, 185, 190, 117, 185, 190, 201, 201, 201, 201, 117, 117, 59, 59, 59, 26, 26, 26, 6, 4, 1, 1, 1, 1, 1, 1, 26, 26, 59, 190, 190, 190, 190, 190, 190, 185, 190, 190, 201, 201, 201, 117, 59, 59, 59, 59, 26, 6, 6, 4, 4, 59, 59] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 739 number of broken/clashed sets: 35 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113680 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `2' /scratch/stefan/7770410/working/building/REAL300020113680/2 /scratch/stefan/7770410/working/building/REAL300020113680 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 2 (index: 971) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/971 `/scratch/stefan/7770410/working/3D/971' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)C(CN1C=CC=N1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113680.mol2' -> `2.mol2' `temp.mol2' -> `REAL300020113680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113680/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113680 none C[NH+](C)C(CN1C=CC=N1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 8, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [13, 11, 13, 13, 6, 11, 18, 24, 24, 24, 24, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 31, 35, 46, 46, 46, 46, 7, 7, 1, 13, 13, 13, 13, 13, 13, 11, 18, 18, 24, 24, 24, 6, 1, 1, 1, 1, 7, 31, 31, 35, 35, 1, 1] 101 rigid atoms, others: [45, 43, 44, 13, 14, 15, 16, 17, 52, 46, 29, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 235 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113680 none C[NH+](C)C(CN1C=CC=N1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 8, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [35, 30, 35, 35, 20, 30, 47, 55, 55, 55, 55, 20, 20, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 7, 35, 35, 35, 35, 35, 35, 30, 47, 47, 55, 55, 55, 20, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7] 101 rigid atoms, others: [47, 16, 17, 18, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 279 number of broken/clashed sets: 61 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113680 none C[NH+](C)C(CN1C=CC=N1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 8, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [15, 11, 15, 15, 5, 1, 1, 1, 1, 1, 1, 11, 16, 16, 16, 24, 24, 24, 55, 55, 55, 97, 99, 101, 101, 101, 101, 55, 55, 24, 15, 15, 15, 15, 15, 15, 11, 5, 5, 1, 1, 1, 16, 24, 24, 24, 24, 55, 97, 97, 99, 99, 24, 24] 101 rigid atoms, others: [5, 6, 39, 8, 9, 10, 7, 40, 41] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 361 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113680 none C[NH+](C)C(CN1C=CC=N1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 8, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [95, 89, 95, 95, 79, 89, 99, 101, 101, 101, 101, 79, 79, 49, 49, 49, 25, 25, 25, 7, 4, 1, 1, 1, 1, 1, 1, 25, 25, 49, 95, 95, 95, 95, 95, 95, 89, 99, 99, 101, 101, 101, 79, 49, 49, 49, 49, 25, 7, 7, 4, 4, 49, 49] 101 rigid atoms, others: [21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 384 number of broken/clashed sets: 61 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113680 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113680 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 2: /scratch/stefan/7770410/working/building/REAL300020113680/2.* 1: /scratch/stefan/7770410/working/building/REAL300020113680/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113680/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113680 Building REAL300020113681 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113681' /scratch/stefan/7770410/working/building/REAL300020113681 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113681 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113681/0 /scratch/stefan/7770410/working/building/REAL300020113681 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/972 `/scratch/stefan/7770410/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(F)=C1) `REAL300020113681.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113681 none CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 13, 23, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 45, 62, 77, 77, 77, 77, 11, 11, 1, 13, 13, 13, 23, 23, 23, 23, 23, 23, 13, 13, 6, 1, 1, 1, 1, 11, 45, 45, 62, 62, 1, 1, 13] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49]) total number of confs: 339 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113681 none CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 76, 114, 76, 76, 76, 42, 42, 42, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 14, 14, 14, 14, 1, 1, 11, 76, 76, 76, 114, 114, 114, 114, 114, 114, 76, 76, 42, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 76] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 359 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113681 none CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 76, 76, 76, 151, 185, 201, 201, 201, 201, 76, 76, 13, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 5, 13, 13, 13, 13, 76, 151, 151, 185, 185, 13, 13, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 49, 35, 36, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 709 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113681 none CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 166, 166, 166, 77, 77, 77, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 77, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 166, 77, 77, 77, 77, 14, 6, 6, 4, 4, 77, 77, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 528 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113681 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113681/1 /scratch/stefan/7770410/working/building/REAL300020113681 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 973) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/973 `/scratch/stefan/7770410/working/3D/973' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(F)=C1) `REAL300020113681.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113681/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113681 none CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 13, 23, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 45, 62, 77, 77, 77, 77, 11, 11, 1, 13, 13, 13, 23, 23, 23, 23, 23, 23, 13, 13, 6, 1, 1, 1, 1, 11, 45, 45, 62, 62, 1, 1, 13] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49]) total number of confs: 339 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113681 none CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 76, 114, 76, 76, 76, 42, 42, 42, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 14, 14, 14, 14, 1, 1, 11, 76, 76, 76, 114, 114, 114, 114, 114, 114, 76, 76, 42, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 76] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 359 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113681 none CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 76, 76, 76, 151, 185, 201, 201, 201, 201, 76, 76, 13, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 5, 13, 13, 13, 13, 76, 151, 151, 185, 185, 13, 13, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 49, 35, 36, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 709 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113681 none CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 166, 166, 166, 77, 77, 77, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 77, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 166, 77, 77, 77, 77, 14, 6, 6, 4, 4, 77, 77, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 528 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113681 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113681 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113681/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113681/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113681 Building REAL300020113682 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113682' /scratch/stefan/7770410/working/building/REAL300020113682 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113682 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113682/0 /scratch/stefan/7770410/working/building/REAL300020113682 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/974 `/scratch/stefan/7770410/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)N1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113682.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113682 none CCC(CC)N1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [36, 35, 20, 35, 35, 20, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 13, 21, 21, 21, 21, 21, 5, 5, 1, 36, 36, 36, 36, 36, 35, 35, 35, 35, 35, 35, 20, 20, 6, 1, 1, 1, 1, 5, 13, 13, 21, 21, 1, 1] 88 rigid atoms, others: [45, 44, 43, 12, 13, 14, 15, 16, 52, 46, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 196 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113682 none CCC(CC)N1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 39, 54, 54, 39, 39, 39, 39, 18, 18, 18, 5, 5, 5, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 5, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 39, 39, 18, 5, 5, 5, 5, 1, 5, 5, 7, 7, 5, 5] 88 rigid atoms, others: [15, 47, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 175 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113682 none CCC(CC)N1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 1, 4, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 39, 39, 39, 60, 73, 73, 73, 73, 73, 39, 39, 20, 5, 5, 5, 5, 5, 4, 5, 5, 5, 5, 5, 1, 1, 6, 20, 20, 20, 20, 39, 60, 60, 73, 73, 20, 20] 88 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 40, 41] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 284 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113682 none CCC(CC)N1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 73, 88, 88, 73, 73, 73, 73, 41, 41, 41, 22, 22, 22, 8, 8, 8, 5, 2, 1, 1, 1, 1, 1, 1, 8, 8, 22, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 73, 73, 41, 22, 22, 22, 22, 8, 5, 5, 2, 2, 22, 22] 88 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 256 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113682 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113682/1 /scratch/stefan/7770410/working/building/REAL300020113682 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 975) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/975 `/scratch/stefan/7770410/working/3D/975' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)N1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113682.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113682/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113682 none CCC(CC)N1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [36, 35, 20, 35, 35, 20, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 13, 21, 21, 21, 21, 21, 5, 5, 1, 36, 36, 36, 36, 36, 35, 35, 35, 35, 35, 35, 20, 20, 6, 1, 1, 1, 1, 5, 13, 13, 21, 21, 1, 1] 88 rigid atoms, others: [45, 44, 43, 12, 13, 14, 15, 16, 52, 46, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 196 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113682 none CCC(CC)N1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 39, 54, 54, 39, 39, 39, 39, 18, 18, 18, 5, 5, 5, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 5, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 39, 39, 18, 5, 5, 5, 5, 1, 5, 5, 7, 7, 5, 5] 88 rigid atoms, others: [15, 47, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 175 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113682 none CCC(CC)N1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 1, 4, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 39, 39, 39, 60, 73, 73, 73, 73, 73, 39, 39, 20, 5, 5, 5, 5, 5, 4, 5, 5, 5, 5, 5, 1, 1, 6, 20, 20, 20, 20, 39, 60, 60, 73, 73, 20, 20] 88 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 40, 41] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 284 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113682 none CCC(CC)N1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 73, 88, 88, 73, 73, 73, 73, 41, 41, 41, 22, 22, 22, 8, 8, 8, 5, 2, 1, 1, 1, 1, 1, 1, 8, 8, 22, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 73, 73, 41, 22, 22, 22, 22, 8, 5, 5, 2, 2, 22, 22] 88 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 256 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113682 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113682 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113682/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113682/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113682 Building REAL300020113683 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113683' /scratch/stefan/7770410/working/building/REAL300020113683 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113683 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113683/0 /scratch/stefan/7770410/working/building/REAL300020113683 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/976 `/scratch/stefan/7770410/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)SC2=N1) `REAL300020113683.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113683 none CC1=CN2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)SC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 27, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 62, 81, 101, 101, 101, 101, 12, 12, 1, 27, 27, 27, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 12, 62, 62, 81, 81, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 388 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113683 none CC1=CN2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)SC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 110, 110, 50, 50, 50, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 18, 18, 18, 18, 1, 1, 12, 110, 110, 110, 110, 110, 110, 110, 110, 50, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 266 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113683 none CC1=CN2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)SC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 27, 27, 27, 110, 110, 110, 169, 201, 201, 201, 201, 201, 110, 110, 27, 1, 1, 1, 2, 2, 2, 1, 1, 8, 27, 27, 27, 27, 110, 169, 169, 201, 201, 27, 27] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 25, 26, 27, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 667 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113683 none CC1=CN2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)SC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 167, 167, 167, 101, 101, 101, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 101, 201, 201, 201, 201, 201, 201, 201, 201, 167, 101, 101, 101, 101, 18, 6, 6, 4, 4, 101, 101] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 512 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113683 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113683/1 /scratch/stefan/7770410/working/building/REAL300020113683 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 977) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/977 `/scratch/stefan/7770410/working/3D/977' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)SC2=N1) `REAL300020113683.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113683 none CC1=CN2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)SC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 28, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 61, 80, 100, 100, 100, 100, 12, 12, 1, 28, 28, 28, 28, 28, 28, 28, 28, 6, 1, 1, 1, 1, 12, 61, 61, 80, 80, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 386 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113683 none CC1=CN2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)SC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 109, 109, 109, 49, 49, 49, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 18, 18, 18, 18, 1, 1, 12, 109, 109, 109, 109, 109, 109, 109, 109, 49, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 262 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113683 none CC1=CN2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)SC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 28, 28, 28, 109, 109, 109, 169, 201, 201, 201, 201, 201, 109, 109, 28, 1, 1, 1, 2, 2, 2, 1, 1, 8, 28, 28, 28, 28, 109, 169, 169, 201, 201, 28, 28] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 25, 26, 27, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 673 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113683 none CC1=CN2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)SC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 168, 168, 168, 102, 102, 102, 19, 19, 19, 6, 4, 1, 1, 1, 1, 1, 1, 19, 19, 102, 201, 201, 201, 201, 201, 201, 201, 201, 168, 102, 102, 102, 102, 19, 6, 6, 4, 4, 102, 102] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 511 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113683 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113683 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113683/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113683/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113683 Building REAL300020113684 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113684' /scratch/stefan/7770410/working/building/REAL300020113684 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113684 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113684/0 /scratch/stefan/7770410/working/building/REAL300020113684 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/978 `/scratch/stefan/7770410/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1) `REAL300020113684.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113684 none CC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 16, 20, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 36, 50, 57, 57, 57, 57, 11, 11, 1, 16, 16, 20, 20, 20, 20, 20, 20, 20, 16, 16, 6, 1, 1, 1, 1, 11, 36, 36, 50, 50, 1, 1, 16] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49]) total number of confs: 259 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113684 none CC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 83, 90, 83, 83, 83, 30, 30, 30, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 83, 83, 90, 90, 90, 90, 90, 90, 90, 83, 83, 30, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 83] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 235 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113684 none CC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 83, 83, 83, 158, 200, 201, 201, 201, 201, 83, 83, 16, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 5, 16, 16, 16, 16, 83, 158, 158, 200, 200, 16, 16, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 49, 35, 36, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 767 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113684 none CC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 101, 101, 101, 58, 58, 58, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 58, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 101, 58, 58, 58, 58, 13, 6, 6, 4, 4, 58, 58, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 445 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113684 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113684/1 /scratch/stefan/7770410/working/building/REAL300020113684 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 979) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/979 `/scratch/stefan/7770410/working/3D/979' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1) `REAL300020113684.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113684 none CC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 16, 20, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 36, 50, 57, 57, 57, 57, 11, 11, 1, 16, 16, 20, 20, 20, 20, 20, 20, 20, 16, 16, 6, 1, 1, 1, 1, 11, 36, 36, 50, 50, 1, 1, 16] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49]) total number of confs: 259 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113684 none CC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 83, 90, 83, 83, 83, 30, 30, 30, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 83, 83, 90, 90, 90, 90, 90, 90, 90, 83, 83, 30, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 83] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 235 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113684 none CC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 83, 83, 83, 158, 200, 201, 201, 201, 201, 83, 83, 16, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 5, 16, 16, 16, 16, 83, 158, 158, 200, 200, 16, 16, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 49, 35, 36, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 767 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113684 none CC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 102, 102, 102, 59, 59, 59, 14, 14, 14, 7, 4, 1, 1, 1, 1, 1, 1, 14, 14, 59, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 102, 59, 59, 59, 59, 14, 7, 7, 4, 4, 59, 59, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 450 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113684 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113684 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113684/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113684/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113684 Building REAL300020113685 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113685' /scratch/stefan/7770410/working/building/REAL300020113685 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for REAL300020113685 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113685/0 /scratch/stefan/7770410/working/building/REAL300020113685 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/980 `/scratch/stefan/7770410/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[N@@H+]1CCCC1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113685.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113685 none CC(C)[N@@H+]1CCCC1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [26, 21, 26, 21, 21, 21, 21, 21, 17, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 9, 9, 9, 9, 9, 9, 8, 8, 1, 26, 26, 26, 26, 26, 26, 26, 21, 21, 21, 21, 21, 21, 21, 17, 17, 6, 1, 1, 1, 1, 8, 9, 9, 9, 9, 1, 1] 49 rigid atoms, others: [16, 12, 13, 46, 15, 48, 49, 14, 55, 56, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53, 54]) total number of confs: 121 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113685 none CC(C)[N@@H+]1CCCC1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 45, 49, 45, 45, 45, 45, 45, 42, 26, 26, 26, 8, 8, 8, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 8, 49, 49, 49, 49, 49, 49, 49, 45, 45, 45, 45, 45, 45, 45, 42, 42, 26, 8, 8, 8, 8, 1, 4, 4, 4, 4, 8, 8] 49 rigid atoms, others: [50, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56]) total number of confs: 199 number of broken/clashed sets: 49 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113685 none CC(C)[N@@H+]1CCCC1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 21, 21, 21, 45, 45, 45, 46, 46, 46, 46, 46, 46, 45, 45, 21, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 21, 21, 21, 21, 45, 46, 46, 46, 46, 21, 21] 49 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 41, 42, 39, 40, 9, 36, 38, 37] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 113 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113685 none CC(C)[N@@H+]1CCCC1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 37, 39, 37, 37, 37, 37, 37, 35, 25, 25, 25, 10, 10, 10, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 39, 39, 39, 39, 39, 39, 39, 37, 37, 37, 37, 37, 37, 37, 35, 35, 25, 10, 10, 10, 10, 4, 3, 3, 1, 1, 10, 10] 39 rigid atoms, others: [22, 19, 20, 21, 54, 23, 24, 25, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 55, 56]) total number of confs: 144 number of broken/clashed sets: 39 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113685 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113685/1 /scratch/stefan/7770410/working/building/REAL300020113685 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 981) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/981 `/scratch/stefan/7770410/working/3D/981' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[N@H+]1CCCC1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113685.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113685/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113685 none CC(C)[N@H+]1CCCC1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 15, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 8, 5, 5, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 15, 15, 5, 1, 1, 1, 1, 5, 8, 8, 8, 8, 1, 1] 20 rigid atoms, others: [16, 12, 13, 46, 15, 48, 49, 14, 55, 56, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53, 54]) total number of confs: 84 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113685 none CC(C)[N@H+]1CCCC1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 17, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 17, 17, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 5] 20 rigid atoms, others: [50, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56]) total number of confs: 85 number of broken/clashed sets: 9 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113685 none CC(C)[N@H+]1CCCC1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 4, 10, 10, 10, 17, 17, 17, 18, 18, 18, 20, 20, 20, 20, 20, 20, 18, 18, 17, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 17, 17, 17, 17, 18, 20, 20, 20, 20, 17, 17] 20 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 41, 42, 39, 40, 9, 36, 38, 37] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 75 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113685 none CC(C)[N@H+]1CCCC1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 13, 13, 13, 10, 10, 10, 7, 7, 7, 5, 2, 1, 1, 1, 1, 1, 1, 7, 7, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 13, 10, 10, 10, 10, 7, 5, 5, 2, 2, 10, 10] 19 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 78 number of broken/clashed sets: 10 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113685 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `2' /scratch/stefan/7770410/working/building/REAL300020113685/2 /scratch/stefan/7770410/working/building/REAL300020113685 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 2 (index: 982) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/982 `/scratch/stefan/7770410/working/3D/982' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[N@@H+]1CCCC1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113685.mol2' -> `2.mol2' `temp.mol2' -> `REAL300020113685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113685/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113685 none CC(C)[N@@H+]1CCCC1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [26, 21, 26, 21, 21, 21, 21, 21, 17, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 9, 9, 9, 9, 9, 9, 8, 8, 1, 26, 26, 26, 26, 26, 26, 26, 21, 21, 21, 21, 21, 21, 21, 17, 17, 6, 1, 1, 1, 1, 8, 9, 9, 9, 9, 1, 1] 49 rigid atoms, others: [16, 12, 13, 46, 15, 48, 49, 14, 55, 56, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53, 54]) total number of confs: 121 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113685 none CC(C)[N@@H+]1CCCC1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 45, 49, 45, 45, 45, 45, 45, 42, 26, 26, 26, 8, 8, 8, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 8, 49, 49, 49, 49, 49, 49, 49, 45, 45, 45, 45, 45, 45, 45, 42, 42, 26, 8, 8, 8, 8, 1, 4, 4, 4, 4, 8, 8] 49 rigid atoms, others: [50, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56]) total number of confs: 199 number of broken/clashed sets: 49 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113685 none CC(C)[N@@H+]1CCCC1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 21, 21, 21, 45, 45, 45, 46, 46, 46, 46, 46, 46, 45, 45, 21, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 21, 21, 21, 21, 45, 46, 46, 46, 46, 21, 21] 49 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 41, 42, 39, 40, 9, 36, 38, 37] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 113 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113685 none CC(C)[N@@H+]1CCCC1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 37, 39, 37, 37, 37, 37, 37, 35, 25, 25, 25, 10, 10, 10, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 39, 39, 39, 39, 39, 39, 39, 37, 37, 37, 37, 37, 37, 37, 35, 35, 25, 10, 10, 10, 10, 4, 3, 3, 1, 1, 10, 10] 39 rigid atoms, others: [22, 19, 20, 21, 54, 23, 24, 25, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 55, 56]) total number of confs: 144 number of broken/clashed sets: 39 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113685 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `3' /scratch/stefan/7770410/working/building/REAL300020113685/3 /scratch/stefan/7770410/working/building/REAL300020113685 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 3 (index: 983) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/983 `/scratch/stefan/7770410/working/3D/983' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[N@H+]1CCCC1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113685.mol2' -> `3.mol2' `temp.mol2' -> `REAL300020113685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113685/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113685 none CC(C)[N@H+]1CCCC1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 15, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 8, 5, 5, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 15, 15, 5, 1, 1, 1, 1, 5, 8, 8, 8, 8, 1, 1] 20 rigid atoms, others: [16, 12, 13, 46, 15, 48, 49, 14, 55, 56, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53, 54]) total number of confs: 84 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113685 none CC(C)[N@H+]1CCCC1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 17, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 17, 17, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 5] 20 rigid atoms, others: [50, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56]) total number of confs: 85 number of broken/clashed sets: 9 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113685 none CC(C)[N@H+]1CCCC1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 4, 10, 10, 10, 17, 17, 17, 18, 18, 18, 20, 20, 20, 20, 20, 20, 18, 18, 17, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 17, 17, 17, 17, 18, 20, 20, 20, 20, 17, 17] 20 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 41, 42, 39, 40, 9, 36, 38, 37] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 75 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113685 none CC(C)[N@H+]1CCCC1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 13, 13, 13, 10, 10, 10, 7, 7, 7, 5, 2, 1, 1, 1, 1, 1, 1, 7, 7, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 13, 10, 10, 10, 10, 7, 5, 5, 2, 2, 10, 10] 19 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 78 number of broken/clashed sets: 10 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113685 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113685 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 2: /scratch/stefan/7770410/working/building/REAL300020113685/2.* 1: /scratch/stefan/7770410/working/building/REAL300020113685/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113685/0.* 3: /scratch/stefan/7770410/working/building/REAL300020113685/3.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113685 Building REAL300020113686 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113686' /scratch/stefan/7770410/working/building/REAL300020113686 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113686 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113686/0 /scratch/stefan/7770410/working/building/REAL300020113686 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/984 `/scratch/stefan/7770410/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC[N@@H+]1C1CCCC1) `REAL300020113686.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113686 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC[N@@H+]1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 8, 8, 1, 3, 3, 3, 3, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 16 rigid atoms, others: [35, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 52 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113686 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC[N@@H+]1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 3, 7, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 3, 7, 7, 7, 7, 16, 16, 16, 16, 16, 7, 7, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 16 rigid atoms, others: [57, 55, 49, 50, 51, 52, 53, 54, 23, 56, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 32 number of broken/clashed sets: 6 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113686 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC[N@@H+]1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 8, 8, 8, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 8, 8, 3, 3, 3, 1, 1, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 16 rigid atoms, others: [38, 39, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 50 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113686 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC[N@@H+]1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 16 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 40, 41, 34, 18, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 25 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113686 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC[N@@H+]1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 3, 7, 7, 7, 7, 16, 16, 16, 16, 16, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 16 rigid atoms, others: [1, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 34 number of broken/clashed sets: 6 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113686 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113686/1 /scratch/stefan/7770410/working/building/REAL300020113686 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 985) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/985 `/scratch/stefan/7770410/working/3D/985' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC[N@H+]1C1CCCC1) `REAL300020113686.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113686 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC[N@H+]1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 7, 7, 7, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 7, 18, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 18, 7, 7, 7, 7, 1, 3, 3, 3, 3, 7, 7, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 22 rigid atoms, others: [35, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 74 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113686 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC[N@H+]1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 3, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 3, 8, 8, 8, 8, 22, 22, 22, 22, 22, 8, 8, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 22 rigid atoms, others: [57, 55, 49, 50, 51, 52, 53, 54, 23, 56, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 42 number of broken/clashed sets: 7 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113686 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC[N@H+]1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 7, 7, 7, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 18, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 18, 7, 7, 7, 7, 3, 3, 3, 1, 1, 7, 7, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 22 rigid atoms, others: [38, 39, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 72 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113686 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC[N@H+]1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 22 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 40, 41, 34, 18, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 30 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113686 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC[N@H+]1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 3, 8, 8, 8, 8, 22, 22, 22, 22, 22, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 22 rigid atoms, others: [1, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 44 number of broken/clashed sets: 7 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113686 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113686 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113686/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113686/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113686 Building REAL300020113687 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113687' /scratch/stefan/7770410/working/building/REAL300020113687 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113687 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113687/0 /scratch/stefan/7770410/working/building/REAL300020113687 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/986 `/scratch/stefan/7770410/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CSC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113687.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113687 none O=C(CCC1=CSC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 14, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 19, 25, 41, 41, 41, 41, 1, 1, 1, 1, 1, 7, 7, 7, 19, 31, 31, 31, 31, 31, 7, 7, 1, 19, 19, 25, 25, 41, 41, 41, 3, 1, 1, 1, 1, 7, 19, 19, 31, 31, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 262 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113687 none O=C(CCC1=CSC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 14, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 58, 69, 119, 119, 119, 119, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 58, 58, 69, 69, 119, 119, 119, 13, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 403 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113687 none O=C(CCC1=CSC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 14, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 6, 2, 1, 1, 1, 1, 1, 1, 23, 23, 41, 41, 41, 119, 119, 119, 168, 201, 201, 201, 201, 201, 119, 119, 41, 6, 6, 2, 2, 1, 1, 1, 23, 41, 41, 41, 41, 119, 168, 168, 201, 201, 41, 41] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 722 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113687 none O=C(CCC1=CSC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 14, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 109, 118, 201, 201, 201, 201, 31, 31, 31, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 31, 109, 109, 118, 118, 201, 201, 201, 46, 31, 31, 31, 31, 7, 4, 4, 2, 2, 31, 31] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 624 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113687 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113687/1 /scratch/stefan/7770410/working/building/REAL300020113687 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 987) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/987 `/scratch/stefan/7770410/working/3D/987' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CSC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113687.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113687/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113687 none O=C(CCC1=CSC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 14, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 19, 25, 41, 41, 41, 41, 1, 1, 1, 1, 1, 7, 7, 7, 19, 31, 31, 31, 31, 31, 7, 7, 1, 19, 19, 25, 25, 41, 41, 41, 3, 1, 1, 1, 1, 7, 19, 19, 31, 31, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 262 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113687 none O=C(CCC1=CSC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 14, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 57, 68, 118, 118, 118, 118, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 57, 57, 68, 68, 118, 118, 118, 13, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 400 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113687 none O=C(CCC1=CSC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 14, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 6, 2, 1, 1, 1, 1, 1, 1, 23, 23, 41, 41, 41, 118, 118, 118, 167, 201, 201, 201, 201, 201, 118, 118, 41, 6, 6, 2, 2, 1, 1, 1, 23, 41, 41, 41, 41, 118, 167, 167, 201, 201, 41, 41] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 726 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113687 none O=C(CCC1=CSC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 14, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 109, 118, 201, 201, 201, 201, 32, 32, 32, 8, 8, 8, 5, 2, 1, 1, 1, 1, 1, 1, 8, 8, 32, 109, 109, 118, 118, 201, 201, 201, 45, 32, 32, 32, 32, 8, 5, 5, 2, 2, 32, 32] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 625 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113687 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113687 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113687/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113687/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113687 Building REAL300020113688 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113688' /scratch/stefan/7770410/working/building/REAL300020113688 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113688 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113688/0 /scratch/stefan/7770410/working/building/REAL300020113688 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/988 `/scratch/stefan/7770410/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC2=CC=CC=C2N=C1) `REAL300020113688.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113688 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC2=CC=CC=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 13, 58, 84, 84, 84, 84, 84, 84, 84, 84, 84, 58, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13, 84, 84, 84, 84, 84] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 240 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113688 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC2=CC=CC=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 92, 92, 92, 16, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 92, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 92, 92, 92, 92, 16, 6, 6, 4, 4, 92, 92, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 548 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113688 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC2=CC=CC=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 56, 78, 92, 92, 92, 92, 13, 13, 1, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 13, 56, 56, 78, 78, 1, 1, 12, 12, 12, 12, 12] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113688 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC2=CC=CC=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 12, 12, 12, 84, 84, 84, 167, 201, 201, 201, 201, 201, 84, 84, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 12, 12, 12, 12, 84, 167, 167, 201, 201, 12, 12, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 734 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113688 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113688/1 /scratch/stefan/7770410/working/building/REAL300020113688 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 989) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/989 `/scratch/stefan/7770410/working/3D/989' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC2=CC=CC=C2N=C1) `REAL300020113688.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113688 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC2=CC=CC=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 13, 58, 84, 84, 84, 84, 84, 84, 84, 84, 84, 58, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13, 84, 84, 84, 84, 84] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 240 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113688 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC2=CC=CC=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 91, 91, 91, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 91, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 91, 91, 91, 91, 15, 6, 6, 4, 4, 91, 91, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 549 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113688 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC2=CC=CC=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 56, 78, 92, 92, 92, 92, 13, 13, 1, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 13, 56, 56, 78, 78, 1, 1, 12, 12, 12, 12, 12] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113688 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC2=CC=CC=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 12, 12, 12, 84, 84, 84, 167, 201, 201, 201, 201, 201, 84, 84, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 12, 12, 12, 12, 84, 167, 167, 201, 201, 12, 12, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 731 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113688 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113688 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113688/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113688/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113688 Building REAL300020113689 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113689' /scratch/stefan/7770410/working/building/REAL300020113689 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113689 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113689/0 /scratch/stefan/7770410/working/building/REAL300020113689 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/990 `/scratch/stefan/7770410/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(F)C(F)=C1) `REAL300020113689.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113689 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(F)C(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 15, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 24, 70, 70, 70, 70, 70, 70, 70, 24, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 70, 70, 70] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 160 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113689 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(F)C(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 15, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 48, 48, 48, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 48, 77, 201, 201, 201, 201, 201, 201, 201, 77, 48, 48, 48, 48, 11, 6, 6, 4, 4, 48, 48, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 399 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113689 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(F)C(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 15, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 31, 44, 47, 47, 47, 47, 9, 9, 1, 5, 15, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 9, 31, 31, 44, 44, 1, 1, 15, 15, 15] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113689 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(F)C(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 15, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 15, 15, 15, 70, 70, 70, 145, 201, 201, 201, 201, 201, 70, 70, 15, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 70, 145, 145, 201, 201, 15, 15, 1, 1, 1] 201 rigid atoms, others: [1, 39, 40, 41, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 837 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113689 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113689/1 /scratch/stefan/7770410/working/building/REAL300020113689 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 991) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/991 `/scratch/stefan/7770410/working/3D/991' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(F)C(F)=C1) `REAL300020113689.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113689/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113689 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(F)C(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 15, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 24, 69, 69, 69, 69, 69, 69, 69, 24, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 69, 69, 69] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 159 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113689 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(F)C(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 15, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 48, 48, 48, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 48, 76, 201, 201, 201, 201, 201, 201, 201, 76, 48, 48, 48, 48, 11, 6, 6, 4, 4, 48, 48, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 398 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113689 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(F)C(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 15, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 31, 44, 48, 48, 48, 48, 9, 9, 1, 5, 14, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 9, 31, 31, 44, 44, 1, 1, 14, 14, 14] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113689 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(F)C(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 15, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 14, 14, 14, 69, 69, 69, 144, 201, 201, 201, 201, 201, 69, 69, 14, 1, 1, 1, 1, 1, 1, 1, 1, 5, 14, 14, 14, 14, 69, 144, 144, 201, 201, 14, 14, 1, 1, 1] 201 rigid atoms, others: [1, 39, 40, 41, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 841 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113689 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113689 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113689/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113689/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113689 Building REAL300020113690 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113690' /scratch/stefan/7770410/working/building/REAL300020113690 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113690 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113690/0 /scratch/stefan/7770410/working/building/REAL300020113690 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/992 `/scratch/stefan/7770410/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(F)=CC=C1F) `REAL300020113690.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113690 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(F)=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 15, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 8, 12, 16, 16, 16, 16, 1, 1, 6, 20, 78, 78, 78, 78, 78, 78, 78, 20, 6, 6, 6, 6, 1, 8, 8, 12, 12, 6, 6, 78, 69, 78] 152 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 189 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113690 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(F)=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 15, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 44, 44, 44, 21, 21, 21, 7, 4, 1, 1, 1, 1, 1, 1, 21, 21, 44, 73, 153, 153, 153, 153, 153, 153, 153, 73, 44, 44, 44, 44, 21, 7, 7, 4, 4, 44, 44, 153, 153, 153] 153 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 333 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113690 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(F)=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 15, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 23, 34, 43, 43, 43, 43, 6, 6, 1, 6, 41, 41, 41, 41, 41, 41, 41, 6, 1, 1, 1, 1, 6, 23, 23, 34, 34, 1, 1, 41, 31, 41] 152 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113690 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(F)=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 15, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 41, 41, 41, 78, 78, 78, 138, 152, 152, 152, 152, 152, 78, 78, 41, 1, 1, 1, 1, 1, 1, 1, 1, 12, 41, 41, 41, 41, 78, 138, 138, 152, 152, 41, 41, 1, 1, 1] 152 rigid atoms, others: [1, 39, 40, 41, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 548 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113690 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113690/1 /scratch/stefan/7770410/working/building/REAL300020113690 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 993) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/993 `/scratch/stefan/7770410/working/3D/993' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(F)=CC=C1F) `REAL300020113690.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113690/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113690 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(F)=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 15, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 8, 12, 16, 16, 16, 16, 1, 1, 6, 21, 78, 78, 78, 78, 78, 78, 78, 21, 6, 6, 6, 6, 1, 8, 8, 12, 12, 6, 6, 78, 69, 78] 152 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 190 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113690 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(F)=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 15, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 45, 45, 45, 21, 21, 21, 7, 4, 1, 1, 1, 1, 1, 1, 21, 21, 45, 74, 152, 152, 152, 152, 152, 152, 152, 74, 45, 45, 45, 45, 21, 7, 7, 4, 4, 45, 45, 152, 152, 152] 152 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 333 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113690 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(F)=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 15, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 23, 34, 44, 44, 44, 44, 6, 6, 1, 6, 42, 42, 42, 42, 42, 42, 42, 6, 1, 1, 1, 1, 6, 23, 23, 34, 34, 1, 1, 42, 32, 42] 152 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113690 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(F)=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 15, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 42, 42, 42, 78, 78, 78, 138, 152, 152, 152, 152, 152, 78, 78, 42, 1, 1, 1, 1, 1, 1, 1, 1, 12, 42, 42, 42, 42, 78, 138, 138, 152, 152, 42, 42, 1, 1, 1] 152 rigid atoms, others: [1, 39, 40, 41, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 551 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113690 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113690 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113690/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113690/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113690 Building REAL300020113691 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113691' /scratch/stefan/7770410/working/building/REAL300020113691 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113691 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113691/0 /scratch/stefan/7770410/working/building/REAL300020113691 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/994 `/scratch/stefan/7770410/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1C2CC3CC(C2)CC1C3) `REAL300020113691.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113691 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1C2CC3CC(C2)CC1C3 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 1, 1, 11, 42, 99, 99, 99, 99, 99, 99, 99, 99, 99, 42, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 336 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113691 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1C2CC3CC(C2)CC1C3 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 68, 68, 68, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 68, 139, 201, 201, 201, 201, 201, 201, 201, 201, 201, 139, 68, 68, 68, 68, 13, 6, 6, 4, 4, 68, 68, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 637 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113691 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1C2CC3CC(C2)CC1C3 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 42, 60, 68, 68, 68, 68, 11, 11, 1, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 11, 42, 42, 60, 60, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113691 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1C2CC3CC(C2)CC1C3 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 17, 17, 17, 99, 99, 99, 166, 201, 201, 201, 201, 201, 99, 99, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 17, 17, 17, 17, 99, 166, 166, 201, 201, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 702 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113691 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113691/1 /scratch/stefan/7770410/working/building/REAL300020113691 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 995) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/995 `/scratch/stefan/7770410/working/3D/995' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1C2CC3CC(C2)CC1C3) `REAL300020113691.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113691/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113691 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1C2CC3CC(C2)CC1C3 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 1, 1, 11, 42, 99, 99, 99, 99, 99, 99, 99, 99, 99, 42, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 336 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113691 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1C2CC3CC(C2)CC1C3 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 69, 69, 69, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 69, 139, 201, 201, 201, 201, 201, 201, 201, 201, 201, 139, 69, 69, 69, 69, 13, 6, 6, 4, 4, 69, 69, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 635 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113691 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1C2CC3CC(C2)CC1C3 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 42, 60, 68, 68, 68, 68, 11, 11, 1, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 11, 42, 42, 60, 60, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113691 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1C2CC3CC(C2)CC1C3 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 17, 17, 17, 99, 99, 99, 166, 201, 201, 201, 201, 201, 99, 99, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 17, 17, 17, 17, 99, 166, 166, 201, 201, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 702 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113691 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113691 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113691/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113691/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113691 Building REAL300020113692 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113692' /scratch/stefan/7770410/working/building/REAL300020113692 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113692 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113692/0 /scratch/stefan/7770410/working/building/REAL300020113692 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/996 `/scratch/stefan/7770410/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NO1) `REAL300020113692.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113692 none CC1=CC(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 58, 28, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 32, 49, 57, 57, 57, 57, 10, 10, 1, 64, 64, 64, 64, 64, 64, 28, 28, 6, 1, 1, 1, 1, 10, 32, 32, 49, 49, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 372 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113692 none CC1=CC(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [138, 138, 138, 134, 99, 38, 38, 38, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 10, 138, 138, 138, 138, 138, 138, 99, 99, 38, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 461 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113692 none CC1=CC(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 4, 14, 31, 31, 31, 64, 64, 64, 138, 138, 138, 187, 201, 201, 201, 201, 201, 138, 138, 64, 1, 1, 2, 2, 2, 1, 14, 14, 31, 64, 64, 64, 64, 138, 187, 187, 201, 201, 64, 64] 201 rigid atoms, others: [0, 1, 2, 3, 4, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 655 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113692 none CC1=CC(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 196, 136, 136, 136, 59, 59, 59, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 59, 201, 201, 201, 201, 201, 201, 196, 196, 136, 59, 59, 59, 59, 10, 6, 6, 4, 4, 59, 59] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 685 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113692 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113692/1 /scratch/stefan/7770410/working/building/REAL300020113692 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 997) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/997 `/scratch/stefan/7770410/working/3D/997' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NO1) `REAL300020113692.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113692 none CC1=CC(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 59, 28, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 32, 49, 57, 57, 57, 57, 10, 10, 1, 65, 65, 65, 65, 65, 65, 28, 28, 6, 1, 1, 1, 1, 10, 32, 32, 49, 49, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 374 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113692 none CC1=CC(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [138, 138, 138, 134, 99, 38, 38, 38, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 10, 138, 138, 138, 138, 138, 138, 99, 99, 38, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 461 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113692 none CC1=CC(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 4, 14, 32, 32, 32, 65, 65, 65, 138, 138, 138, 187, 201, 201, 201, 201, 201, 138, 138, 65, 1, 1, 2, 2, 2, 1, 14, 14, 32, 65, 65, 65, 65, 138, 187, 187, 201, 201, 65, 65] 201 rigid atoms, others: [0, 1, 2, 3, 4, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 656 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113692 none CC1=CC(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 196, 136, 136, 136, 59, 59, 59, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 59, 201, 201, 201, 201, 201, 201, 196, 196, 136, 59, 59, 59, 59, 10, 6, 6, 4, 4, 59, 59] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 688 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113692 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113692 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113692/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113692/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113692 Building REAL300020113693 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113693' /scratch/stefan/7770410/working/building/REAL300020113693 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113693 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113693/0 /scratch/stefan/7770410/working/building/REAL300020113693 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/998 `/scratch/stefan/7770410/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1F) `REAL300020113693.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113693 none COC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 16, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 24, 37, 37, 37, 37, 37, 8, 8, 1, 16, 16, 16, 26, 26, 26, 16, 16, 6, 1, 1, 1, 1, 8, 24, 24, 37, 37, 1, 1, 16] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45]) total number of confs: 199 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113693 none COC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 65, 65, 65, 65, 24, 24, 24, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 65, 65, 65, 93, 93, 93, 65, 65, 24, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 65] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 207 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113693 none COC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 65, 65, 65, 144, 201, 201, 201, 201, 201, 65, 65, 16, 1, 1, 1, 3, 3, 3, 1, 1, 5, 16, 16, 16, 16, 65, 144, 144, 201, 201, 16, 16, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 45, 25, 26, 27, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 820 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113693 none COC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 69, 69, 69, 40, 40, 40, 10, 10, 10, 4, 2, 1, 1, 1, 1, 1, 1, 10, 10, 40, 201, 201, 201, 201, 201, 201, 201, 201, 69, 40, 40, 40, 40, 10, 4, 4, 2, 2, 40, 40, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 370 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113693 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113693/1 /scratch/stefan/7770410/working/building/REAL300020113693 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 999) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/999 `/scratch/stefan/7770410/working/3D/999' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1F) `REAL300020113693.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113693 none COC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 16, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 24, 37, 37, 37, 37, 37, 8, 8, 1, 16, 16, 16, 26, 26, 26, 16, 16, 6, 1, 1, 1, 1, 8, 24, 24, 37, 37, 1, 1, 16] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45]) total number of confs: 199 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113693 none COC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 65, 65, 65, 65, 24, 24, 24, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 65, 65, 65, 92, 92, 92, 65, 65, 24, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 65] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 205 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113693 none COC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 65, 65, 65, 143, 201, 201, 201, 201, 201, 65, 65, 16, 1, 1, 1, 3, 3, 3, 1, 1, 5, 16, 16, 16, 16, 65, 143, 143, 201, 201, 16, 16, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 45, 25, 26, 27, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 823 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113693 none COC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 69, 69, 69, 40, 40, 40, 10, 10, 10, 4, 2, 1, 1, 1, 1, 1, 1, 10, 10, 40, 201, 201, 201, 201, 201, 201, 201, 201, 69, 40, 40, 40, 40, 10, 4, 4, 2, 2, 40, 40, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 370 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113693 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113693 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113693/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113693/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113693 Building REAL300020113694 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113694' /scratch/stefan/7770410/working/building/REAL300020113694 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113694 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113694/0 /scratch/stefan/7770410/working/building/REAL300020113694 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1000 `/scratch/stefan/7770410/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C(C)C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113694.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113694 none CC1=NOC(C(C)C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 29, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 26, 39, 39, 39, 39, 39, 11, 11, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 11, 26, 26, 39, 39, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 14, 15, 48, 49, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 196 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113694 none CC1=NOC(C(C)C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 104, 104, 104, 104, 104, 32, 32, 32, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 11, 104, 104, 104, 104, 104, 104, 104, 104, 104, 104, 32, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [43, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 206 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113694 none CC1=NOC(C(C)C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 10, 10, 10, 29, 29, 29, 104, 104, 104, 161, 201, 201, 201, 201, 201, 104, 104, 29, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 29, 29, 29, 29, 104, 161, 161, 201, 201, 29, 29] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 716 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113694 none CC1=NOC(C(C)C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 83, 83, 83, 39, 39, 39, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 39, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 83, 39, 39, 39, 39, 8, 4, 4, 2, 2, 39, 39] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 407 number of broken/clashed sets: 2 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113694 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113694/1 /scratch/stefan/7770410/working/building/REAL300020113694 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1001) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1001 `/scratch/stefan/7770410/working/3D/1001' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C(C)C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113694.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113694 none CC1=NOC(C(C)C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 26, 39, 39, 39, 39, 39, 11, 11, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 1, 1, 1, 1, 11, 26, 26, 39, 39, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 14, 15, 48, 49, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 195 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113694 none CC1=NOC(C(C)C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 104, 104, 104, 104, 104, 32, 32, 32, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 11, 104, 104, 104, 104, 104, 104, 104, 104, 104, 104, 32, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [43, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 207 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113694 none CC1=NOC(C(C)C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 10, 10, 10, 28, 28, 28, 104, 104, 104, 161, 201, 201, 201, 201, 201, 104, 104, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 28, 28, 28, 28, 104, 161, 161, 201, 201, 28, 28] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 716 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113694 none CC1=NOC(C(C)C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 82, 82, 82, 39, 39, 39, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 39, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 82, 39, 39, 39, 39, 8, 4, 4, 2, 2, 39, 39] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 405 number of broken/clashed sets: 2 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113694 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113694 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113694/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113694/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113694 Building REAL300020113695 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113695' /scratch/stefan/7770410/working/building/REAL300020113695 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113695 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113695/0 /scratch/stefan/7770410/working/building/REAL300020113695 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1002) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1002 `/scratch/stefan/7770410/working/3D/1002' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC2=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=NN2C=C1) `REAL300020113695.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113695 none CC1=CC2=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=NN2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 30, 45, 51, 51, 51, 51, 11, 11, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 11, 30, 30, 45, 45, 1, 1, 26, 26, 26] 201 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 228 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113695 none CC1=CC2=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=NN2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 100, 33, 33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 100, 100, 100, 100, 100, 100, 100, 100, 100, 33, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 100, 100, 100] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 205 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113695 none CC1=CC2=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=NN2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 9, 26, 26, 26, 100, 100, 100, 161, 201, 201, 201, 201, 201, 100, 100, 26, 1, 1, 1, 1, 1, 2, 2, 2, 1, 9, 26, 26, 26, 26, 100, 161, 161, 201, 201, 26, 26, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 45, 46, 47, 24, 25, 26, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 739 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113695 none CC1=CC2=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=NN2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 106, 106, 106, 53, 53, 53, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 53, 201, 201, 201, 201, 201, 201, 201, 201, 201, 106, 53, 53, 53, 53, 11, 6, 6, 4, 4, 53, 53, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 455 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113695 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113695/1 /scratch/stefan/7770410/working/building/REAL300020113695 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1003) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1003 `/scratch/stefan/7770410/working/3D/1003' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC2=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=NN2C=C1) `REAL300020113695.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113695 none CC1=CC2=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=NN2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 30, 45, 51, 51, 51, 51, 11, 11, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 1, 1, 1, 1, 11, 30, 30, 45, 45, 1, 1, 28, 28, 28] 201 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 230 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113695 none CC1=CC2=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=NN2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 102, 33, 33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 102, 102, 102, 102, 102, 102, 102, 102, 102, 33, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 102, 102, 102] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 207 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113695 none CC1=CC2=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=NN2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 9, 28, 28, 28, 102, 102, 102, 162, 201, 201, 201, 201, 201, 102, 102, 28, 1, 1, 1, 1, 1, 2, 2, 2, 1, 9, 28, 28, 28, 28, 102, 162, 162, 201, 201, 28, 28, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 45, 46, 47, 24, 25, 26, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 731 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113695 none CC1=CC2=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=NN2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 107, 107, 107, 54, 54, 54, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 54, 201, 201, 201, 201, 201, 201, 201, 201, 201, 107, 54, 54, 54, 54, 11, 6, 6, 4, 4, 54, 54, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 458 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113695 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113695 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113695/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113695/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113695 Building REAL300020113696 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113696' /scratch/stefan/7770410/working/building/REAL300020113696 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113696 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113696/0 /scratch/stefan/7770410/working/building/REAL300020113696 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1004) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1004 `/scratch/stefan/7770410/working/3D/1004' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C2CC2)N=NS1) `REAL300020113696.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113696 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C2CC2)N=NS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 8, 8, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 13, 13, 13, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 1, 1, 13, 60, 135, 135, 167, 167, 135, 135, 135, 60, 13, 13, 13, 13, 1, 3, 3, 5, 5, 13, 13, 167, 167, 167, 167, 167] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 407 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113696 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C2CC2)N=NS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 8, 8, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 8, 20, 20, 54, 54, 54, 167, 167, 167, 184, 201, 201, 201, 201, 201, 167, 167, 54, 8, 1, 1, 1, 1, 8, 8, 7, 20, 54, 54, 54, 54, 167, 184, 184, 201, 201, 54, 54, 1, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 43, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 489 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113696 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C2CC2)N=NS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 8, 8, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 34, 34, 34, 5, 5, 5, 4, 2, 1, 1, 1, 1, 1, 1, 5, 5, 34, 105, 178, 178, 201, 201, 178, 178, 178, 105, 34, 34, 34, 34, 5, 4, 4, 2, 2, 34, 34, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 481 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113696 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C2CC2)N=NS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 8, 8, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 22, 34, 34, 34, 34, 34, 13, 13, 1, 6, 28, 28, 54, 54, 28, 28, 28, 6, 1, 1, 1, 1, 13, 22, 22, 34, 34, 1, 1, 54, 54, 54, 54, 54] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43]) total number of confs: 273 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113696 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C2CC2)N=NS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 8, 8, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 28, 28, 28, 135, 135, 135, 156, 178, 178, 178, 178, 178, 135, 135, 28, 1, 1, 1, 8, 8, 1, 1, 1, 8, 28, 28, 28, 28, 135, 156, 156, 178, 178, 28, 28, 8, 8, 8, 8, 8] 201 rigid atoms, others: [1, 19, 20, 21, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 477 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113696 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113696/1 /scratch/stefan/7770410/working/building/REAL300020113696 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1005) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1005 `/scratch/stefan/7770410/working/3D/1005' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C2CC2)N=NS1) `REAL300020113696.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113696 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C2CC2)N=NS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 8, 8, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 13, 13, 13, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 1, 1, 13, 61, 137, 137, 168, 168, 137, 137, 137, 61, 13, 13, 13, 13, 1, 3, 3, 5, 5, 13, 13, 168, 168, 168, 168, 168] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 406 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113696 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C2CC2)N=NS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 8, 8, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 8, 20, 20, 54, 54, 54, 168, 168, 168, 184, 201, 201, 201, 201, 201, 168, 168, 54, 8, 1, 1, 1, 1, 8, 8, 7, 20, 54, 54, 54, 54, 168, 184, 184, 201, 201, 54, 54, 1, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 43, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 485 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113696 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C2CC2)N=NS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 8, 8, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 34, 34, 34, 5, 5, 5, 4, 2, 1, 1, 1, 1, 1, 1, 5, 5, 34, 105, 178, 178, 201, 201, 178, 178, 178, 105, 34, 34, 34, 34, 5, 4, 4, 2, 2, 34, 34, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 481 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113696 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C2CC2)N=NS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 8, 8, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 22, 34, 34, 34, 34, 34, 13, 13, 1, 6, 28, 28, 54, 54, 28, 28, 28, 6, 1, 1, 1, 1, 13, 22, 22, 34, 34, 1, 1, 54, 54, 54, 54, 54] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43]) total number of confs: 273 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113696 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C2CC2)N=NS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 8, 8, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 28, 28, 28, 137, 137, 137, 156, 178, 178, 178, 178, 178, 137, 137, 28, 1, 1, 1, 8, 8, 1, 1, 1, 8, 28, 28, 28, 28, 137, 156, 156, 178, 178, 28, 28, 8, 8, 8, 8, 8] 201 rigid atoms, others: [1, 19, 20, 21, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 467 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113696 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113696 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113696/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113696/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113696 Building REAL300020113697 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113697' /scratch/stefan/7770410/working/building/REAL300020113697 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113697 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113697/0 /scratch/stefan/7770410/working/building/REAL300020113697 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1006) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1006 `/scratch/stefan/7770410/working/3D/1006' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Cl)C=NC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113697.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113697 none CC1=C(Cl)C=NC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 18, 26, 26, 26, 26, 26, 6, 6, 1, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 6, 18, 18, 26, 26, 1, 1] 77 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 43, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 136 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113697 none CC1=C(Cl)C=NC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 46, 46, 46, 46, 17, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 1, 1, 6, 46, 46, 46, 46, 46, 17, 6, 6, 6, 6, 1, 8, 8, 10, 10, 6, 6] 77 rigid atoms, others: [37, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 120 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113697 none CC1=C(Cl)C=NC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 23, 23, 23, 46, 46, 46, 67, 77, 77, 77, 77, 77, 46, 46, 23, 2, 2, 2, 1, 1, 10, 23, 23, 23, 23, 46, 67, 67, 77, 77, 23, 23] 77 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 272 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113697 none CC1=C(Cl)C=NC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 78, 78, 78, 78, 43, 43, 43, 27, 27, 27, 12, 12, 12, 6, 2, 1, 1, 1, 1, 1, 1, 12, 12, 27, 78, 78, 78, 78, 78, 43, 27, 27, 27, 27, 12, 6, 6, 2, 2, 27, 27] 78 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 188 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113697 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113697/1 /scratch/stefan/7770410/working/building/REAL300020113697 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1007) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1007 `/scratch/stefan/7770410/working/3D/1007' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Cl)C=NC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113697.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113697 none CC1=C(Cl)C=NC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 18, 26, 26, 26, 26, 26, 6, 6, 1, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 6, 18, 18, 26, 26, 1, 1] 76 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 43, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 136 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113697 none CC1=C(Cl)C=NC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 45, 45, 45, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 1, 1, 6, 45, 45, 45, 45, 45, 16, 6, 6, 6, 6, 1, 8, 8, 10, 10, 6, 6] 76 rigid atoms, others: [37, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 118 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113697 none CC1=C(Cl)C=NC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 23, 23, 23, 45, 45, 45, 66, 76, 76, 76, 76, 76, 45, 45, 23, 2, 2, 2, 1, 1, 10, 23, 23, 23, 23, 45, 66, 66, 76, 76, 23, 23] 76 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 270 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113697 none CC1=C(Cl)C=NC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 76, 76, 76, 76, 42, 42, 42, 27, 27, 27, 12, 12, 12, 6, 2, 1, 1, 1, 1, 1, 1, 12, 12, 27, 76, 76, 76, 76, 76, 42, 27, 27, 27, 27, 12, 6, 6, 2, 2, 27, 27] 76 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 185 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113697 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113697 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113697/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113697/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113697 Building REAL300020113698 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113698' /scratch/stefan/7770410/working/building/REAL300020113698 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113698 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113698/0 /scratch/stefan/7770410/working/building/REAL300020113698 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1008) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1008 `/scratch/stefan/7770410/working/3D/1008' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(N)=O)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113698.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113698 none CC(C)(C(N)=O)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [20, 12, 20, 20, 27, 27, 12, 12, 10, 10, 10, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 10, 20, 20, 20, 20, 20, 20, 27, 27, 12, 10, 10, 10, 10, 1, 3, 3, 3, 3, 10, 10] 27 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 102 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113698 none CC(C)(C(N)=O)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 13, 13, 8, 8, 6, 6, 6, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 8, 8, 8, 8, 8, 8, 13, 13, 8, 6, 6, 6, 6, 3, 3, 3, 1, 1, 6, 6] 13 rigid atoms, others: [41, 42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44]) total number of confs: 48 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113698 none CC(C)(C(N)=O)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 11, 11, 17, 17, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 11, 11, 11, 11, 11, 11, 17, 17, 5, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1] 27 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113698 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113698/1 /scratch/stefan/7770410/working/building/REAL300020113698 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1009) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1009 `/scratch/stefan/7770410/working/3D/1009' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(N)=O)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113698.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113698/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113698 none CC(C)(C(N)=O)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [20, 12, 20, 20, 27, 27, 12, 12, 10, 10, 10, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 10, 20, 20, 20, 20, 20, 20, 27, 27, 12, 10, 10, 10, 10, 1, 3, 3, 3, 3, 10, 10] 27 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 102 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113698 none CC(C)(C(N)=O)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 13, 13, 8, 8, 6, 6, 6, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 8, 8, 8, 8, 8, 8, 13, 13, 8, 6, 6, 6, 6, 3, 3, 3, 1, 1, 6, 6] 13 rigid atoms, others: [41, 42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44]) total number of confs: 48 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113698 none CC(C)(C(N)=O)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 11, 11, 17, 17, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 11, 11, 11, 11, 11, 11, 17, 17, 5, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1] 27 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113698 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113698 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113698/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113698/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113698 Building REAL300020113699 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113699' /scratch/stefan/7770410/working/building/REAL300020113699 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113699 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113699/0 /scratch/stefan/7770410/working/building/REAL300020113699 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1010) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1010 `/scratch/stefan/7770410/working/3D/1010' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC2=CC=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=C2O1) `REAL300020113699.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113699 none CC1=NC2=CC=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 29, 43, 44, 44, 44, 44, 9, 9, 1, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 9, 29, 29, 43, 43, 1, 1, 13] 201 rigid atoms, others: [45, 35, 36, 37, 38, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46]) total number of confs: 198 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113699 none CC1=NC2=CC=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 71, 71, 24, 24, 24, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 9, 71, 71, 71, 71, 71, 71, 71, 71, 24, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 71] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 159 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113699 none CC1=NC2=CC=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 71, 71, 71, 146, 201, 201, 201, 201, 201, 71, 71, 13, 1, 1, 1, 2, 2, 2, 1, 1, 5, 13, 13, 13, 13, 71, 146, 146, 201, 201, 13, 13, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 46, 33, 27, 28, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 827 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113699 none CC1=NC2=CC=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 78, 78, 78, 45, 45, 45, 10, 10, 10, 6, 3, 1, 1, 1, 1, 1, 1, 10, 10, 45, 201, 201, 201, 201, 201, 201, 201, 201, 78, 45, 45, 45, 45, 10, 6, 6, 3, 3, 45, 45, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 404 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113699 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113699/1 /scratch/stefan/7770410/working/building/REAL300020113699 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1011) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1011 `/scratch/stefan/7770410/working/3D/1011' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC2=CC=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=C2O1) `REAL300020113699.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113699/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113699 none CC1=NC2=CC=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 29, 43, 44, 44, 44, 44, 9, 9, 1, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 9, 29, 29, 43, 43, 1, 1, 13] 201 rigid atoms, others: [45, 35, 36, 37, 38, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46]) total number of confs: 198 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113699 none CC1=NC2=CC=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 71, 71, 24, 24, 24, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 9, 71, 71, 71, 71, 71, 71, 71, 71, 24, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 71] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 159 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113699 none CC1=NC2=CC=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 71, 71, 71, 146, 201, 201, 201, 201, 201, 71, 71, 13, 1, 1, 1, 2, 2, 2, 1, 1, 5, 13, 13, 13, 13, 71, 146, 146, 201, 201, 13, 13, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 46, 33, 27, 28, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 827 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113699 none CC1=NC2=CC=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 78, 78, 78, 45, 45, 45, 10, 10, 10, 6, 3, 1, 1, 1, 1, 1, 1, 10, 10, 45, 201, 201, 201, 201, 201, 201, 201, 201, 78, 45, 45, 45, 45, 10, 6, 6, 3, 3, 45, 45, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 404 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113699 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113699 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113699/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113699/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113699 Building REAL300020113700 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113700' /scratch/stefan/7770410/working/building/REAL300020113700 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113700 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113700/0 /scratch/stefan/7770410/working/building/REAL300020113700 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1012) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1012 `/scratch/stefan/7770410/working/3D/1012' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2OC(=O)NC2=C1) `REAL300020113700.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113700 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2OC(=O)NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 1, 11, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 9, 27, 74, 74, 74, 74, 74, 74, 74, 74, 74, 27, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 74, 74, 74, 74] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 168 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113700 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2OC(=O)NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 1, 11, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 46, 46, 46, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 46, 82, 201, 201, 201, 201, 201, 201, 201, 201, 201, 82, 46, 46, 46, 46, 9, 5, 5, 3, 3, 46, 46, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 414 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113700 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2OC(=O)NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 1, 11, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 30, 45, 46, 46, 46, 46, 9, 9, 1, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 9, 30, 30, 45, 45, 1, 1, 18, 18, 18, 18] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113700 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2OC(=O)NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 1, 11, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 18, 18, 18, 74, 74, 74, 146, 201, 201, 201, 201, 201, 74, 74, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 18, 18, 18, 18, 74, 146, 146, 201, 201, 18, 18, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 806 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113700 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113700/1 /scratch/stefan/7770410/working/building/REAL300020113700 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1013) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1013 `/scratch/stefan/7770410/working/3D/1013' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2OC(=O)NC2=C1) `REAL300020113700.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113700/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113700 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2OC(=O)NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 1, 11, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 9, 28, 75, 75, 75, 75, 75, 75, 75, 75, 75, 28, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 75, 75, 75, 75] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 170 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113700 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2OC(=O)NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 1, 11, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 46, 46, 46, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 46, 82, 201, 201, 201, 201, 201, 201, 201, 201, 201, 82, 46, 46, 46, 46, 9, 5, 5, 3, 3, 46, 46, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 414 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113700 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2OC(=O)NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 1, 11, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 30, 45, 46, 46, 46, 46, 9, 9, 1, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 9, 30, 30, 45, 45, 1, 1, 18, 18, 18, 18] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113700 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2OC(=O)NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 1, 11, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 18, 18, 18, 75, 75, 75, 146, 201, 201, 201, 201, 201, 75, 75, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 18, 18, 18, 18, 75, 146, 146, 201, 201, 18, 18, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 802 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113700 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113700 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113700/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113700/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113700 Building REAL300020113701 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113701' /scratch/stefan/7770410/working/building/REAL300020113701 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300020113701 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113701/0 /scratch/stefan/7770410/working/building/REAL300020113701 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1014) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1014 `/scratch/stefan/7770410/working/3D/1014' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[NH+](C)C) `REAL300020113701.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113701 none CC(C)[C@@H](C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [11, 12, 12, 9, 12, 9, 9, 5, 5, 5, 1, 1, 1, 1, 1, 7, 9, 12, 12, 12, 12, 1, 1, 5, 12, 15, 15, 14, 12, 12, 12, 12, 12, 12, 12, 9, 5, 5, 5, 5, 1, 7, 7, 9, 9, 5, 5, 15, 15, 15, 15, 15, 15] 19 rigid atoms, others: [40, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 111 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113701 none CC(C)[C@@H](C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 18, 19, 18, 18, 14, 14, 14, 13, 13, 13, 8, 4, 1, 1, 1, 1, 1, 1, 13, 13, 14, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 18, 14, 14, 14, 14, 13, 8, 8, 4, 4, 14, 14, 19, 19, 19, 19, 19, 19] 19 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 68 number of broken/clashed sets: 19 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113701 none CC(C)[C@@H](C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [8, 9, 9, 6, 9, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 9, 10, 13, 13, 13, 13, 5, 5, 1, 9, 12, 12, 11, 9, 9, 9, 9, 9, 9, 9, 6, 1, 1, 1, 1, 5, 9, 9, 10, 10, 1, 1, 12, 12, 12, 12, 12, 12] 19 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 45, 46, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52]) total number of confs: 97 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113701 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113701 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 0: /scratch/stefan/7770410/working/building/REAL300020113701/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113701 Building REAL300020113702 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113702' /scratch/stefan/7770410/working/building/REAL300020113702 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113702 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113702/0 /scratch/stefan/7770410/working/building/REAL300020113702 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1015) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1015 `/scratch/stefan/7770410/working/3D/1015' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N(C)C=N1) `REAL300020113702.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113702 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N(C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 5, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 11, 18, 18, 18, 18, 18, 5, 5, 1, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 5, 11, 11, 18, 18, 1, 1, 14, 14, 14, 14] 33 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 39, 40, 21, 30, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 100 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113702 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N(C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 5, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 15, 15, 15, 5, 5, 5, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 5, 24, 24, 24, 24, 24, 24, 24, 15, 5, 5, 5, 5, 1, 6, 6, 8, 8, 5, 5, 24, 24, 24, 24] 33 rigid atoms, others: [34, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 86 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113702 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N(C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 5, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 24, 24, 24, 29, 33, 33, 33, 33, 33, 24, 24, 14, 1, 1, 1, 1, 2, 2, 2, 5, 14, 14, 14, 14, 24, 29, 29, 33, 33, 14, 14, 2, 2, 2, 1] 33 rigid atoms, others: [0, 1, 2, 3, 44, 22, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113702 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N(C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 5, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 26, 26, 26, 19, 19, 19, 9, 9, 9, 5, 2, 1, 1, 1, 1, 1, 1, 9, 9, 19, 33, 33, 33, 33, 33, 33, 33, 26, 19, 19, 19, 19, 9, 5, 5, 2, 2, 19, 19, 33, 33, 33, 33] 33 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 91 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113702 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113702/1 /scratch/stefan/7770410/working/building/REAL300020113702 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1016) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1016 `/scratch/stefan/7770410/working/3D/1016' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N(C)C=N1) `REAL300020113702.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113702/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113702 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N(C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 5, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 11, 18, 18, 18, 18, 18, 5, 5, 1, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 5, 11, 11, 18, 18, 1, 1, 14, 14, 14, 14] 32 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 39, 40, 21, 30, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 100 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113702 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N(C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 5, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 15, 15, 15, 5, 5, 5, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 5, 24, 24, 24, 24, 24, 24, 24, 15, 5, 5, 5, 5, 1, 6, 6, 8, 8, 5, 5, 24, 24, 24, 24] 32 rigid atoms, others: [34, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 86 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113702 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N(C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 5, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 24, 24, 24, 29, 32, 32, 32, 32, 32, 24, 24, 14, 1, 1, 1, 1, 2, 2, 2, 5, 14, 14, 14, 14, 24, 29, 29, 32, 32, 14, 14, 2, 2, 2, 1] 32 rigid atoms, others: [0, 1, 2, 3, 44, 22, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113702 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N(C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 5, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 25, 25, 25, 19, 19, 19, 9, 9, 9, 5, 2, 1, 1, 1, 1, 1, 1, 9, 9, 19, 32, 32, 32, 32, 32, 32, 32, 25, 19, 19, 19, 19, 9, 5, 5, 2, 2, 19, 19, 32, 32, 32, 32] 32 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 87 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113702 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113702 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113702/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113702/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113702 Building REAL300020113703 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113703' /scratch/stefan/7770410/working/building/REAL300020113703 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113703 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113703/0 /scratch/stefan/7770410/working/building/REAL300020113703 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1017) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1017 `/scratch/stefan/7770410/working/3D/1017' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1F) `REAL300020113703.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113703 none CC1=CC(F)=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 41, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 38, 50, 64, 64, 64, 64, 7, 7, 1, 41, 41, 41, 41, 41, 41, 41, 6, 1, 1, 1, 1, 7, 38, 38, 50, 50, 1, 1, 41] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 271 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113703 none CC1=CC(F)=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 98, 98, 29, 29, 29, 7, 7, 7, 1, 1, 1, 1, 1, 9, 13, 18, 18, 18, 18, 1, 1, 7, 98, 98, 98, 98, 98, 98, 98, 29, 7, 7, 7, 7, 1, 9, 9, 13, 13, 7, 7, 98] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 222 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113703 none CC1=CC(F)=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 41, 41, 41, 98, 98, 98, 181, 201, 201, 201, 201, 201, 98, 98, 41, 1, 1, 1, 2, 2, 2, 1, 13, 41, 41, 41, 41, 98, 181, 181, 201, 201, 41, 41, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 44, 25, 26, 27, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 729 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113703 none CC1=CC(F)=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 137, 137, 137, 70, 70, 70, 24, 24, 24, 6, 4, 1, 1, 1, 1, 1, 1, 24, 24, 70, 201, 201, 201, 201, 201, 201, 201, 137, 70, 70, 70, 70, 24, 6, 6, 4, 4, 70, 70, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 475 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113703 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113703/1 /scratch/stefan/7770410/working/building/REAL300020113703 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1018) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1018 `/scratch/stefan/7770410/working/3D/1018' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1F) `REAL300020113703.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113703 none CC1=CC(F)=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 41, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 38, 50, 64, 64, 64, 64, 7, 7, 1, 41, 41, 41, 41, 41, 41, 41, 6, 1, 1, 1, 1, 7, 38, 38, 50, 50, 1, 1, 41] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 271 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113703 none CC1=CC(F)=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 98, 98, 29, 29, 29, 7, 7, 7, 1, 1, 1, 1, 1, 9, 13, 18, 18, 18, 18, 1, 1, 7, 98, 98, 98, 98, 98, 98, 98, 29, 7, 7, 7, 7, 1, 9, 9, 13, 13, 7, 7, 98] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 222 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113703 none CC1=CC(F)=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 41, 41, 41, 98, 98, 98, 181, 201, 201, 201, 201, 201, 98, 98, 41, 1, 1, 1, 2, 2, 2, 1, 13, 41, 41, 41, 41, 98, 181, 181, 201, 201, 41, 41, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 44, 25, 26, 27, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 729 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113703 none CC1=CC(F)=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 137, 137, 137, 70, 70, 70, 24, 24, 24, 6, 4, 1, 1, 1, 1, 1, 1, 24, 24, 70, 201, 201, 201, 201, 201, 201, 201, 137, 70, 70, 70, 70, 24, 6, 6, 4, 4, 70, 70, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 475 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113703 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113703 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113703/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113703/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113703 Building REAL300020113704 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113704' /scratch/stefan/7770410/working/building/REAL300020113704 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113704 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113704/0 /scratch/stefan/7770410/working/building/REAL300020113704 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1019) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1019 `/scratch/stefan/7770410/working/3D/1019' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCC1=CSC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113704.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113704 none O=C(CCCC1=CSC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 14, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 23, 27, 35, 64, 64, 64, 64, 1, 1, 1, 1, 1, 8, 8, 8, 16, 24, 24, 24, 24, 24, 8, 8, 1, 23, 23, 35, 35, 35, 35, 64, 64, 64, 5, 1, 1, 1, 1, 8, 16, 16, 24, 24, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 349 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113704 none O=C(CCCC1=CSC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 14, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 72, 78, 101, 171, 171, 171, 171, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 72, 72, 101, 101, 101, 101, 171, 171, 171, 18, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 726 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113704 none O=C(CCCC1=CSC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 14, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 6, 2, 2, 1, 1, 1, 1, 1, 1, 34, 34, 64, 64, 64, 171, 171, 171, 190, 201, 201, 201, 201, 201, 171, 171, 64, 6, 6, 2, 2, 2, 2, 1, 1, 1, 34, 64, 64, 64, 64, 171, 190, 190, 201, 201, 64, 64] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 523 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113704 none O=C(CCCC1=CSC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 14, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 101, 99, 126, 201, 201, 201, 201, 24, 24, 24, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 24, 101, 101, 126, 126, 126, 126, 201, 201, 201, 31, 24, 24, 24, 24, 7, 4, 4, 2, 2, 24, 24] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 824 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113704 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113704/1 /scratch/stefan/7770410/working/building/REAL300020113704 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1020) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1020 `/scratch/stefan/7770410/working/3D/1020' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCC1=CSC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113704.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113704 none O=C(CCCC1=CSC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 14, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 23, 27, 35, 64, 64, 64, 64, 1, 1, 1, 1, 1, 8, 8, 8, 16, 24, 24, 24, 24, 24, 8, 8, 1, 23, 23, 35, 35, 35, 35, 64, 64, 64, 5, 1, 1, 1, 1, 8, 16, 16, 24, 24, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 349 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113704 none O=C(CCCC1=CSC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 14, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 72, 78, 101, 172, 172, 172, 172, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 72, 72, 101, 101, 101, 101, 172, 172, 172, 18, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 728 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113704 none O=C(CCCC1=CSC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 14, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 6, 2, 2, 1, 1, 1, 1, 1, 1, 34, 34, 64, 64, 64, 172, 172, 172, 190, 201, 201, 201, 201, 201, 172, 172, 64, 6, 6, 2, 2, 2, 2, 1, 1, 1, 34, 64, 64, 64, 64, 172, 190, 190, 201, 201, 64, 64] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 518 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113704 none O=C(CCCC1=CSC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 14, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 101, 99, 126, 201, 201, 201, 201, 23, 23, 23, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 23, 101, 101, 126, 126, 126, 126, 201, 201, 201, 30, 23, 23, 23, 23, 7, 4, 4, 2, 2, 23, 23] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 823 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113704 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113704 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113704/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113704/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113704 Building REAL300020113705 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113705' /scratch/stefan/7770410/working/building/REAL300020113705 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113705 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113705/0 /scratch/stefan/7770410/working/building/REAL300020113705 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1021) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1021 `/scratch/stefan/7770410/working/3D/1021' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2C=CNC2=N1) `REAL300020113705.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113705 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2C=CNC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 20, 20, 20, 20, 1, 1, 13, 54, 89, 89, 89, 89, 89, 89, 89, 89, 54, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 89, 89, 89, 89, 89] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 259 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113705 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2C=CNC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [192, 192, 108, 108, 108, 22, 22, 22, 6, 4, 1, 1, 1, 1, 1, 1, 22, 22, 108, 192, 201, 201, 201, 201, 201, 201, 201, 201, 192, 108, 108, 108, 108, 22, 6, 6, 4, 4, 108, 108, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 543 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113705 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2C=CNC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 66, 87, 106, 106, 106, 106, 13, 13, 1, 6, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 66, 66, 87, 87, 1, 1, 16, 16, 16, 16, 16] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 397 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113705 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2C=CNC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 16, 16, 16, 89, 89, 89, 169, 201, 201, 201, 201, 201, 89, 89, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 89, 169, 169, 201, 201, 16, 16, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 708 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113705 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113705/1 /scratch/stefan/7770410/working/building/REAL300020113705 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1022) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1022 `/scratch/stefan/7770410/working/3D/1022' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2C=CNC2=N1) `REAL300020113705.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113705/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113705 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2C=CNC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 21, 21, 21, 21, 1, 1, 13, 52, 85, 85, 85, 85, 85, 85, 85, 85, 52, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 85, 85, 85, 85, 85] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 253 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113705 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2C=CNC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [192, 192, 109, 109, 109, 23, 23, 23, 6, 4, 1, 1, 1, 1, 1, 1, 23, 23, 109, 192, 201, 201, 201, 201, 201, 201, 201, 201, 192, 109, 109, 109, 109, 23, 6, 6, 4, 4, 109, 109, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 540 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113705 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2C=CNC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 65, 86, 108, 108, 108, 108, 13, 13, 1, 6, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 65, 65, 86, 86, 1, 1, 16, 16, 16, 16, 16] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 400 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113705 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2C=CNC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 16, 16, 16, 85, 85, 85, 167, 201, 201, 201, 201, 201, 85, 85, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 85, 167, 167, 201, 201, 16, 16, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 725 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113705 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113705 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113705/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113705/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113705 Building REAL300020113706 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113706' /scratch/stefan/7770410/working/building/REAL300020113706 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113706 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113706/0 /scratch/stefan/7770410/working/building/REAL300020113706 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1023) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1023 `/scratch/stefan/7770410/working/3D/1023' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2NC=CC2=C1) `REAL300020113706.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113706 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2NC=CC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 34, 82, 82, 82, 82, 82, 82, 82, 82, 34, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9, 82, 82, 82, 82, 82] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 191 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113706 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2NC=CC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 57, 57, 57, 12, 12, 12, 7, 4, 1, 1, 1, 1, 1, 1, 12, 12, 57, 101, 201, 201, 201, 201, 201, 201, 201, 201, 101, 57, 57, 57, 57, 12, 7, 7, 4, 4, 57, 57, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 455 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113706 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2NC=CC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 32, 47, 56, 56, 56, 56, 9, 9, 1, 6, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 9, 32, 32, 47, 47, 1, 1, 17, 17, 17, 17, 17] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113706 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2NC=CC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 17, 17, 17, 82, 82, 82, 154, 201, 201, 201, 201, 201, 82, 82, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 17, 17, 17, 17, 82, 154, 154, 201, 201, 17, 17, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 780 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113706 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113706/1 /scratch/stefan/7770410/working/building/REAL300020113706 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1024) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1024 `/scratch/stefan/7770410/working/3D/1024' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2NC=CC2=C1) `REAL300020113706.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113706 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2NC=CC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 34, 82, 82, 82, 82, 82, 82, 82, 82, 34, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9, 82, 82, 82, 82, 82] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 191 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113706 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2NC=CC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 57, 57, 57, 12, 12, 12, 7, 4, 1, 1, 1, 1, 1, 1, 12, 12, 57, 101, 201, 201, 201, 201, 201, 201, 201, 201, 101, 57, 57, 57, 57, 12, 7, 7, 4, 4, 57, 57, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 453 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113706 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2NC=CC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 32, 47, 56, 56, 56, 56, 9, 9, 1, 6, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 9, 32, 32, 47, 47, 1, 1, 17, 17, 17, 17, 17] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113706 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2NC=CC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 17, 17, 17, 82, 82, 82, 154, 201, 201, 201, 201, 201, 82, 82, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 17, 17, 17, 17, 82, 154, 154, 201, 201, 17, 17, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 780 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113706 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113706 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113706/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113706/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113706 Building REAL300020113707 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113707' /scratch/stefan/7770410/working/building/REAL300020113707 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113707 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113707/0 /scratch/stefan/7770410/working/building/REAL300020113707 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1025) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1025 `/scratch/stefan/7770410/working/3D/1025' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CN=CS1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113707.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113707 none O=C(CC1=CN=CS1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 25, 36, 36, 36, 36, 1, 1, 1, 1, 1, 9, 9, 9, 27, 41, 43, 43, 43, 43, 9, 9, 1, 25, 25, 36, 36, 5, 1, 1, 1, 1, 9, 27, 27, 41, 41, 1, 1] 201 rigid atoms, others: [32, 33, 39, 8, 9, 10, 11, 12, 40, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38]) total number of confs: 275 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113707 none O=C(CC1=CN=CS1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 96, 120, 120, 120, 120, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 96, 96, 120, 120, 24, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [34, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 407 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113707 none O=C(CC1=CN=CS1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 3, 1, 1, 1, 1, 1, 1, 20, 20, 36, 36, 36, 120, 120, 120, 173, 201, 201, 201, 201, 201, 120, 120, 36, 3, 3, 1, 1, 20, 36, 36, 36, 36, 120, 173, 173, 201, 201, 36, 36] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 663 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113707 none O=C(CC1=CN=CS1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 171, 201, 201, 201, 201, 44, 44, 44, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 44, 171, 171, 201, 201, 77, 44, 44, 44, 44, 11, 6, 6, 4, 4, 44, 44] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 698 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113707 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113707/1 /scratch/stefan/7770410/working/building/REAL300020113707 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1026) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1026 `/scratch/stefan/7770410/working/3D/1026' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CN=CS1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113707.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113707/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113707 none O=C(CC1=CN=CS1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 25, 35, 35, 35, 35, 1, 1, 1, 1, 1, 9, 9, 9, 27, 41, 43, 43, 43, 43, 9, 9, 1, 25, 25, 35, 35, 5, 1, 1, 1, 1, 9, 27, 27, 41, 41, 1, 1] 201 rigid atoms, others: [32, 33, 39, 8, 9, 10, 11, 12, 40, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38]) total number of confs: 273 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113707 none O=C(CC1=CN=CS1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 95, 120, 120, 120, 120, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 95, 95, 120, 120, 24, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [34, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 406 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113707 none O=C(CC1=CN=CS1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 3, 1, 1, 1, 1, 1, 1, 19, 19, 35, 35, 35, 120, 120, 120, 173, 201, 201, 201, 201, 201, 120, 120, 35, 3, 3, 1, 1, 19, 35, 35, 35, 35, 120, 173, 173, 201, 201, 35, 35] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 662 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113707 none O=C(CC1=CN=CS1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 14, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 170, 201, 201, 201, 201, 43, 43, 43, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 43, 170, 170, 201, 201, 76, 43, 43, 43, 43, 10, 6, 6, 4, 4, 43, 43] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 702 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113707 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113707 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113707/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113707/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113707 Building REAL300020113708 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113708' /scratch/stefan/7770410/working/building/REAL300020113708 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113708 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113708/0 /scratch/stefan/7770410/working/building/REAL300020113708 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1027) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1027 `/scratch/stefan/7770410/working/3D/1027' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(=O)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CN1C) `REAL300020113708.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113708/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113708 none CC1=CC(=O)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 64, 82, 103, 103, 103, 103, 12, 12, 1, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 12, 64, 64, 82, 82, 1, 1, 18, 18, 18, 18] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 381 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113708 none CC1=CC(=O)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 89, 89, 51, 51, 51, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 18, 18, 18, 18, 1, 1, 12, 89, 89, 89, 89, 89, 89, 89, 51, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 89, 89, 89, 89] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 241 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113708 none CC1=CC(=O)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 89, 89, 89, 165, 201, 201, 201, 201, 201, 89, 89, 18, 1, 1, 1, 2, 2, 2, 1, 6, 18, 18, 18, 18, 89, 165, 165, 201, 201, 18, 18, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 44, 25, 26, 27, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 734 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113708 none CC1=CC(=O)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 192, 192, 192, 103, 103, 103, 19, 19, 19, 6, 4, 1, 1, 1, 1, 1, 1, 19, 19, 103, 201, 201, 201, 201, 201, 201, 201, 192, 103, 103, 103, 103, 19, 6, 6, 4, 4, 103, 103, 201, 201, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 548 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113708 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113708/1 /scratch/stefan/7770410/working/building/REAL300020113708 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1028) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1028 `/scratch/stefan/7770410/working/3D/1028' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(=O)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CN1C) `REAL300020113708.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113708/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113708 none CC1=CC(=O)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 63, 81, 102, 102, 102, 102, 12, 12, 1, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 12, 63, 63, 81, 81, 1, 1, 18, 18, 18, 18] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 378 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113708 none CC1=CC(=O)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 89, 89, 51, 51, 51, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 18, 18, 18, 18, 1, 1, 12, 89, 89, 89, 89, 89, 89, 89, 51, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 89, 89, 89, 89] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 242 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113708 none CC1=CC(=O)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 89, 89, 89, 165, 201, 201, 201, 201, 201, 89, 89, 18, 1, 1, 1, 2, 2, 2, 1, 6, 18, 18, 18, 18, 89, 165, 165, 201, 201, 18, 18, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 44, 25, 26, 27, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 733 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113708 none CC1=CC(=O)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 192, 192, 192, 105, 105, 105, 19, 19, 19, 6, 4, 1, 1, 1, 1, 1, 1, 19, 19, 105, 201, 201, 201, 201, 201, 201, 201, 192, 105, 105, 105, 105, 19, 6, 6, 4, 4, 105, 105, 201, 201, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 542 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113708 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113708 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113708/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113708/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113708 Building REAL300020113709 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113709' /scratch/stefan/7770410/working/building/REAL300020113709 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113709 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113709/0 /scratch/stefan/7770410/working/building/REAL300020113709 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1029) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1029 `/scratch/stefan/7770410/working/3D/1029' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(=O)NN=C1) `REAL300020113709.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113709 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(=O)NN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 9, 9, 9, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 9, 34, 87, 87, 87, 87, 87, 87, 34, 9, 9, 9, 9, 1, 8, 8, 10, 10, 9, 9, 87, 87, 87] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 205 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113709 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(=O)NN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 59, 59, 59, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 59, 114, 201, 201, 201, 201, 201, 201, 114, 59, 59, 59, 59, 13, 6, 6, 4, 4, 59, 59, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 472 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113709 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(=O)NN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 31, 47, 57, 57, 57, 57, 9, 9, 1, 6, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 9, 31, 31, 47, 47, 1, 1, 19, 19, 19] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113709 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(=O)NN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 19, 19, 19, 87, 87, 87, 161, 201, 201, 201, 201, 201, 87, 87, 19, 1, 1, 1, 1, 1, 1, 1, 5, 19, 19, 19, 19, 87, 161, 161, 201, 201, 19, 19, 1, 1, 1] 201 rigid atoms, others: [1, 38, 39, 40, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 752 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113709 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113709/1 /scratch/stefan/7770410/working/building/REAL300020113709 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1030) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1030 `/scratch/stefan/7770410/working/3D/1030' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(=O)NN=C1) `REAL300020113709.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113709/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113709 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(=O)NN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 9, 9, 9, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 9, 34, 87, 87, 87, 87, 87, 87, 34, 9, 9, 9, 9, 1, 8, 8, 10, 10, 9, 9, 87, 87, 87] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 205 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113709 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(=O)NN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 59, 59, 59, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 59, 114, 201, 201, 201, 201, 201, 201, 114, 59, 59, 59, 59, 13, 6, 6, 4, 4, 59, 59, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 472 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113709 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(=O)NN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 31, 47, 57, 57, 57, 57, 9, 9, 1, 6, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 9, 31, 31, 47, 47, 1, 1, 19, 19, 19] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113709 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(=O)NN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 19, 19, 19, 87, 87, 87, 161, 201, 201, 201, 201, 201, 87, 87, 19, 1, 1, 1, 1, 1, 1, 1, 5, 19, 19, 19, 19, 87, 161, 161, 201, 201, 19, 19, 1, 1, 1] 201 rigid atoms, others: [1, 38, 39, 40, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 752 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113709 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113709 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113709/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113709/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113709 Building REAL300020113710 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113710' /scratch/stefan/7770410/working/building/REAL300020113710 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113710 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113710/0 /scratch/stefan/7770410/working/building/REAL300020113710 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1031) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1031 `/scratch/stefan/7770410/working/3D/1031' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)NC(=O)N1) `REAL300020113710.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113710 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)NC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 28, 42, 45, 45, 45, 45, 11, 11, 1, 25, 25, 25, 25, 25, 25, 25, 6, 1, 1, 1, 1, 11, 28, 28, 42, 42, 1, 1, 25, 25] 201 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 39, 40, 21, 30, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 213 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113710 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)NC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 29, 29, 29, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 98, 98, 98, 98, 98, 98, 98, 29, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 98, 98] 201 rigid atoms, others: [34, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 200 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113710 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)NC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 8, 8, 8, 25, 25, 25, 98, 98, 98, 154, 201, 201, 201, 201, 201, 98, 98, 25, 1, 1, 1, 1, 2, 2, 2, 8, 25, 25, 25, 25, 98, 154, 154, 201, 201, 25, 25, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 41, 42, 22, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 742 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113710 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)NC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 90, 90, 90, 48, 48, 48, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 48, 201, 201, 201, 201, 201, 201, 201, 90, 48, 48, 48, 48, 11, 6, 6, 4, 4, 48, 48, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 440 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113710 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113710/1 /scratch/stefan/7770410/working/building/REAL300020113710 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1032) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1032 `/scratch/stefan/7770410/working/3D/1032' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)NC(=O)N1) `REAL300020113710.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113710 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)NC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 28, 42, 45, 45, 45, 45, 11, 11, 1, 25, 25, 25, 25, 25, 25, 25, 6, 1, 1, 1, 1, 11, 28, 28, 42, 42, 1, 1, 25, 25] 201 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 39, 40, 21, 30, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 213 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113710 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)NC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 29, 29, 29, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 98, 98, 98, 98, 98, 98, 98, 29, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 98, 98] 201 rigid atoms, others: [34, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 200 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113710 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)NC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 8, 8, 8, 25, 25, 25, 98, 98, 98, 154, 201, 201, 201, 201, 201, 98, 98, 25, 1, 1, 1, 1, 2, 2, 2, 8, 25, 25, 25, 25, 98, 154, 154, 201, 201, 25, 25, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 41, 42, 22, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 742 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113710 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)NC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 90, 90, 90, 48, 48, 48, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 48, 201, 201, 201, 201, 201, 201, 201, 90, 48, 48, 48, 48, 11, 6, 6, 4, 4, 48, 48, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 440 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113710 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113710 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113710/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113710/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113710 Building REAL300020113711 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113711' /scratch/stefan/7770410/working/building/REAL300020113711 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113711 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113711/0 /scratch/stefan/7770410/working/building/REAL300020113711 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1033) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1033 `/scratch/stefan/7770410/working/3D/1033' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC2=NNN=C2C=C1) `REAL300020113711.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113711 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC2=NNN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 8, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 20, 20, 20, 20, 1, 1, 13, 53, 85, 85, 85, 85, 85, 85, 85, 85, 53, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 85, 85, 85] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 251 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113711 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC2=NNN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 8, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [193, 193, 109, 109, 109, 23, 23, 23, 6, 4, 1, 1, 1, 1, 1, 1, 23, 23, 109, 193, 201, 201, 201, 201, 201, 201, 201, 201, 193, 109, 109, 109, 109, 23, 6, 6, 4, 4, 109, 109, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 543 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113711 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC2=NNN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 8, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 67, 89, 109, 109, 109, 109, 13, 13, 1, 6, 16, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 13, 67, 67, 89, 89, 1, 1, 17, 17, 17] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 410 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113711 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC2=NNN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 8, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 17, 17, 17, 85, 85, 85, 168, 201, 201, 201, 201, 201, 85, 85, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 17, 17, 17, 17, 85, 168, 168, 201, 201, 17, 17, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 704 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113711 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113711/1 /scratch/stefan/7770410/working/building/REAL300020113711 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1034) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1034 `/scratch/stefan/7770410/working/3D/1034' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC2=NNN=C2C=C1) `REAL300020113711.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113711/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113711 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC2=NNN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 8, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 19, 19, 19, 19, 1, 1, 13, 54, 89, 89, 89, 89, 89, 89, 89, 89, 54, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 89, 89, 89] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 257 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113711 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC2=NNN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 8, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [194, 194, 112, 112, 112, 23, 23, 23, 6, 4, 1, 1, 1, 1, 1, 1, 23, 23, 112, 194, 201, 201, 201, 201, 201, 201, 201, 201, 194, 112, 112, 112, 112, 23, 6, 6, 4, 4, 112, 112, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 543 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113711 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC2=NNN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 8, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 68, 90, 111, 111, 111, 111, 13, 13, 1, 6, 15, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 68, 68, 90, 90, 1, 1, 16, 16, 16] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 414 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113711 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC2=NNN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 8, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 16, 16, 16, 89, 89, 89, 169, 201, 201, 201, 201, 201, 89, 89, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 89, 169, 169, 201, 201, 16, 16, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 699 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113711 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113711 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113711/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113711/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113711 Building REAL300020113712 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113712' /scratch/stefan/7770410/working/building/REAL300020113712 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113712 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113712/0 /scratch/stefan/7770410/working/building/REAL300020113712 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1035) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1035 `/scratch/stefan/7770410/working/3D/1035' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C2OCCCN2N=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113712.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113712 none CC1=C2OCCCN2N=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 5, 5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 16, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 65, 87, 106, 106, 106, 106, 13, 13, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 13, 65, 65, 87, 87, 1, 1] 201 rigid atoms, others: [48, 39, 40, 41, 42, 12, 13, 14, 15, 16, 49, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 405 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113712 none CC1=C2OCCCN2N=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 5, 5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 87, 87, 87, 87, 87, 87, 54, 54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 20, 20, 20, 20, 1, 1, 13, 87, 87, 87, 87, 87, 87, 87, 87, 87, 54, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13] 201 rigid atoms, others: [43, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 256 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113712 none CC1=C2OCCCN2N=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 5, 5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 87, 87, 87, 163, 201, 201, 201, 201, 201, 87, 87, 17, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 17, 87, 163, 163, 201, 201, 17, 17] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 35, 32, 36, 33, 37] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 720 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113712 none CC1=C2OCCCN2N=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 5, 5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 194, 194, 194, 109, 109, 109, 24, 24, 24, 6, 4, 1, 1, 1, 1, 1, 1, 24, 24, 109, 201, 201, 201, 201, 201, 201, 201, 201, 201, 194, 109, 109, 109, 109, 24, 6, 6, 4, 4, 109, 109] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 538 number of broken/clashed sets: 2 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113712 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113712/1 /scratch/stefan/7770410/working/building/REAL300020113712 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1036) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1036 `/scratch/stefan/7770410/working/3D/1036' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C2OCCCN2N=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113712.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113712 none CC1=C2OCCCN2N=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 5, 5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 16, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 65, 87, 106, 106, 106, 106, 13, 13, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 13, 65, 65, 87, 87, 1, 1] 201 rigid atoms, others: [48, 39, 40, 41, 42, 12, 13, 14, 15, 16, 49, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 405 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113712 none CC1=C2OCCCN2N=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 5, 5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 87, 87, 87, 87, 87, 87, 54, 54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 20, 20, 20, 20, 1, 1, 13, 87, 87, 87, 87, 87, 87, 87, 87, 87, 54, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13] 201 rigid atoms, others: [43, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 256 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113712 none CC1=C2OCCCN2N=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 5, 5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 87, 87, 87, 163, 201, 201, 201, 201, 201, 87, 87, 17, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 17, 87, 163, 163, 201, 201, 17, 17] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 35, 32, 36, 33, 37] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 720 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113712 none CC1=C2OCCCN2N=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 5, 5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 193, 193, 193, 108, 108, 108, 24, 24, 24, 6, 4, 1, 1, 1, 1, 1, 1, 24, 24, 108, 201, 201, 201, 201, 201, 201, 201, 201, 201, 193, 108, 108, 108, 108, 24, 6, 6, 4, 4, 108, 108] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 538 number of broken/clashed sets: 2 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113712 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113712 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113712/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113712/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113712 Building REAL300020113713 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113713' /scratch/stefan/7770410/working/building/REAL300020113713 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113713 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113713/0 /scratch/stefan/7770410/working/building/REAL300020113713 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1037) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1037 `/scratch/stefan/7770410/working/3D/1037' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN2CCCC2=C1) `REAL300020113713.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113713 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN2CCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 20, 20, 20, 20, 1, 1, 13, 51, 83, 83, 83, 83, 83, 83, 83, 51, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 83, 83, 83, 83, 83, 83, 83] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 242 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113713 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN2CCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [194, 194, 114, 114, 114, 23, 23, 23, 6, 4, 1, 1, 1, 1, 1, 1, 23, 23, 114, 194, 201, 201, 201, 201, 201, 201, 201, 194, 114, 114, 114, 114, 23, 6, 6, 4, 4, 114, 114, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 541 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113713 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN2CCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 71, 94, 118, 118, 118, 118, 13, 13, 1, 6, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 13, 71, 71, 94, 94, 1, 1, 21, 21, 21, 21, 21, 21, 21] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 438 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113713 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN2CCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 21, 21, 21, 83, 83, 83, 167, 201, 201, 201, 201, 201, 83, 83, 21, 1, 1, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 21, 83, 167, 167, 201, 201, 21, 21, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 39, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 703 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113713 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113713/1 /scratch/stefan/7770410/working/building/REAL300020113713 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1038) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1038 `/scratch/stefan/7770410/working/3D/1038' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN2CCCC2=C1) `REAL300020113713.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113713 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN2CCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 21, 21, 21, 21, 1, 1, 13, 51, 84, 84, 84, 84, 84, 84, 84, 51, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 84, 84, 84, 84, 84, 84, 84] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 246 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113713 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN2CCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [195, 195, 115, 115, 115, 24, 24, 24, 6, 4, 1, 1, 1, 1, 1, 1, 24, 24, 115, 195, 201, 201, 201, 201, 201, 201, 201, 195, 115, 115, 115, 115, 24, 6, 6, 4, 4, 115, 115, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 540 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113713 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN2CCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 71, 94, 119, 119, 119, 119, 13, 13, 1, 6, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 13, 71, 71, 94, 94, 1, 1, 21, 21, 21, 21, 21, 21, 21] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 440 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113713 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN2CCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 21, 21, 21, 84, 84, 84, 167, 201, 201, 201, 201, 201, 84, 84, 21, 1, 1, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 21, 84, 167, 167, 201, 201, 21, 21, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 39, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 698 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113713 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113713 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113713/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113713/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113713 Building REAL300020113714 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113714' /scratch/stefan/7770410/working/building/REAL300020113714 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113714 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113714/0 /scratch/stefan/7770410/working/building/REAL300020113714 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1039) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1039 `/scratch/stefan/7770410/working/3D/1039' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC=N1) `REAL300020113714.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113714 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 10, 10, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 47, 55, 55, 55, 55, 11, 11, 1, 10, 10, 10, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 31, 31, 47, 47, 1, 1, 10] 201 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43]) total number of confs: 283 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113714 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 59, 59, 33, 33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 11, 59, 59, 59, 97, 97, 97, 97, 97, 33, 11, 11, 11, 11, 1, 5, 5, 7, 7, 11, 11, 59] 201 rigid atoms, others: [36, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 345 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113714 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 59, 59, 59, 136, 193, 201, 201, 201, 201, 59, 59, 10, 1, 1, 1, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 59, 136, 136, 193, 193, 10, 10, 1] 201 rigid atoms, others: [1, 2, 3, 4, 43, 23, 24, 25] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 809 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113714 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 124, 124, 124, 56, 56, 56, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 56, 201, 201, 201, 201, 201, 201, 201, 201, 124, 56, 56, 56, 56, 10, 6, 6, 4, 4, 56, 56, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 485 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113714 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113714/1 /scratch/stefan/7770410/working/building/REAL300020113714 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1040) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1040 `/scratch/stefan/7770410/working/3D/1040' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC=N1) `REAL300020113714.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113714 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 10, 10, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 47, 55, 55, 55, 55, 11, 11, 1, 10, 10, 10, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 31, 31, 47, 47, 1, 1, 10] 201 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43]) total number of confs: 283 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113714 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 59, 59, 33, 33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 11, 59, 59, 59, 97, 97, 97, 97, 97, 33, 11, 11, 11, 11, 1, 5, 5, 7, 7, 11, 11, 59] 201 rigid atoms, others: [36, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 345 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113714 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 59, 59, 59, 136, 193, 201, 201, 201, 201, 59, 59, 10, 1, 1, 1, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 59, 136, 136, 193, 193, 10, 10, 1] 201 rigid atoms, others: [1, 2, 3, 4, 43, 23, 24, 25] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 809 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113714 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 123, 123, 123, 55, 55, 55, 9, 9, 9, 6, 4, 1, 1, 1, 1, 1, 1, 9, 9, 55, 201, 201, 201, 201, 201, 201, 201, 201, 123, 55, 55, 55, 55, 9, 6, 6, 4, 4, 55, 55, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 485 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113714 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113714 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113714/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113714/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113714 Building REAL300020113715 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113715' /scratch/stefan/7770410/working/building/REAL300020113715 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113715 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113715/0 /scratch/stefan/7770410/working/building/REAL300020113715 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1041) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1041 `/scratch/stefan/7770410/working/3D/1041' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NC(C)=NC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113715.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113715 none COC1=NC(C)=NC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 40, 6, 40, 40, 40, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 42, 52, 65, 65, 65, 65, 8, 8, 1, 40, 40, 40, 40, 40, 40, 40, 6, 1, 1, 1, 1, 8, 42, 42, 52, 52, 1, 1] 201 rigid atoms, others: [45, 36, 37, 38, 39, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 352 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113715 none COC1=NC(C)=NC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 95, 30, 95, 95, 95, 30, 30, 30, 8, 8, 8, 1, 1, 1, 1, 1, 9, 11, 18, 18, 18, 18, 1, 1, 8, 95, 95, 95, 95, 95, 95, 95, 30, 8, 8, 8, 8, 1, 9, 9, 11, 11, 8, 8] 201 rigid atoms, others: [40, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 407 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113715 none COC1=NC(C)=NC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 40, 40, 40, 95, 95, 95, 178, 201, 201, 201, 201, 201, 95, 95, 40, 1, 1, 1, 2, 2, 2, 1, 12, 40, 40, 40, 40, 95, 178, 178, 201, 201, 40, 40] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 28, 29, 30] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 723 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113715 none COC1=NC(C)=NC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 134, 201, 201, 201, 134, 134, 134, 68, 68, 68, 23, 23, 23, 6, 4, 1, 1, 1, 1, 1, 1, 23, 23, 68, 201, 201, 201, 201, 201, 201, 201, 134, 68, 68, 68, 68, 23, 6, 6, 4, 4, 68, 68] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 698 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113715 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113715/1 /scratch/stefan/7770410/working/building/REAL300020113715 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1042) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1042 `/scratch/stefan/7770410/working/3D/1042' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NC(C)=NC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113715.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113715 none COC1=NC(C)=NC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 40, 6, 40, 40, 40, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 42, 52, 65, 65, 65, 65, 8, 8, 1, 40, 40, 40, 40, 40, 40, 40, 6, 1, 1, 1, 1, 8, 42, 42, 52, 52, 1, 1] 201 rigid atoms, others: [45, 36, 37, 38, 39, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 352 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113715 none COC1=NC(C)=NC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 95, 30, 95, 95, 95, 30, 30, 30, 8, 8, 8, 1, 1, 1, 1, 1, 9, 11, 18, 18, 18, 18, 1, 1, 8, 95, 95, 95, 95, 95, 95, 95, 30, 8, 8, 8, 8, 1, 9, 9, 11, 11, 8, 8] 201 rigid atoms, others: [40, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 407 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113715 none COC1=NC(C)=NC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 40, 40, 40, 95, 95, 95, 178, 201, 201, 201, 201, 201, 95, 95, 40, 1, 1, 1, 2, 2, 2, 1, 12, 40, 40, 40, 40, 95, 178, 178, 201, 201, 40, 40] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 28, 29, 30] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 723 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113715 none COC1=NC(C)=NC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 135, 201, 201, 201, 135, 135, 135, 69, 69, 69, 24, 24, 24, 6, 4, 1, 1, 1, 1, 1, 1, 24, 24, 69, 201, 201, 201, 201, 201, 201, 201, 135, 69, 69, 69, 69, 24, 6, 6, 4, 4, 69, 69] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 696 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113715 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113715 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113715/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113715/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113715 Building REAL300020113716 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113716' /scratch/stefan/7770410/working/building/REAL300020113716 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113716 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113716/0 /scratch/stefan/7770410/working/building/REAL300020113716 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1043) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1043 `/scratch/stefan/7770410/working/3D/1043' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2CCCN2N=C1) `REAL300020113716.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113716 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2CCCN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 6, 18, 56, 56, 56, 56, 56, 56, 56, 18, 6, 6, 6, 6, 1, 8, 8, 10, 10, 6, 6, 56, 56, 56, 56, 56, 56, 56] 119 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 141 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113716 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2CCCN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 49, 49, 49, 20, 20, 20, 6, 4, 1, 1, 1, 1, 1, 1, 20, 20, 49, 85, 120, 120, 120, 120, 120, 120, 120, 85, 49, 49, 49, 49, 20, 6, 6, 4, 4, 49, 49, 120, 120, 120, 120, 120, 120, 120] 120 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 295 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113716 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2CCCN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 30, 38, 44, 44, 44, 44, 6, 6, 1, 6, 31, 31, 31, 31, 31, 31, 31, 6, 1, 1, 1, 1, 6, 30, 30, 38, 38, 1, 1, 31, 31, 31, 31, 31, 31, 31] 119 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113716 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2CCCN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 31, 31, 31, 56, 56, 56, 105, 119, 119, 119, 119, 119, 56, 56, 31, 1, 1, 1, 1, 1, 1, 1, 1, 10, 31, 31, 31, 31, 56, 105, 105, 119, 119, 31, 31, 1, 1, 1, 1, 1, 1, 1] 119 rigid atoms, others: [1, 39, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 437 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113716 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113716/1 /scratch/stefan/7770410/working/building/REAL300020113716 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1044) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1044 `/scratch/stefan/7770410/working/3D/1044' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2CCCN2N=C1) `REAL300020113716.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113716 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2CCCN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 6, 19, 57, 57, 57, 57, 57, 57, 57, 19, 6, 6, 6, 6, 1, 8, 8, 10, 10, 6, 6, 57, 57, 57, 57, 57, 57, 57] 120 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 143 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113716 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2CCCN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 49, 49, 49, 20, 20, 20, 6, 4, 1, 1, 1, 1, 1, 1, 20, 20, 49, 85, 119, 119, 119, 119, 119, 119, 119, 85, 49, 49, 49, 49, 20, 6, 6, 4, 4, 49, 49, 119, 119, 119, 119, 119, 119, 119] 119 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 293 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113716 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2CCCN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 30, 38, 44, 44, 44, 44, 6, 6, 1, 6, 31, 31, 31, 31, 31, 31, 31, 6, 1, 1, 1, 1, 6, 30, 30, 38, 38, 1, 1, 31, 31, 31, 31, 31, 31, 31] 120 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113716 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2CCCN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 31, 31, 31, 57, 57, 57, 106, 120, 120, 120, 120, 120, 57, 57, 31, 1, 1, 1, 1, 1, 1, 1, 1, 10, 31, 31, 31, 31, 57, 106, 106, 120, 120, 31, 31, 1, 1, 1, 1, 1, 1, 1] 120 rigid atoms, others: [1, 39, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 439 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113716 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113716 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113716/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113716/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113716 Building REAL300020113717 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113717' /scratch/stefan/7770410/working/building/REAL300020113717 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113717 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113717/0 /scratch/stefan/7770410/working/building/REAL300020113717 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1045) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1045 `/scratch/stefan/7770410/working/3D/1045' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1) `REAL300020113717.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113717 none CC(=O)NC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 8, 8, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 47, 67, 78, 78, 78, 78, 13, 13, 1, 8, 8, 13, 13, 13, 13, 8, 8, 6, 1, 1, 1, 1, 13, 47, 47, 67, 67, 1, 1, 8] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47]) total number of confs: 324 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113717 none CC(=O)NC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 56, 56, 56, 56, 50, 50, 50, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 13, 56, 56, 88, 88, 88, 88, 56, 56, 50, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13, 56] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 305 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113717 none CC(=O)NC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 56, 56, 56, 138, 190, 197, 197, 197, 197, 56, 56, 8, 1, 1, 3, 3, 3, 3, 1, 1, 4, 8, 8, 8, 8, 56, 138, 138, 190, 190, 8, 8, 1] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 47, 27, 28] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 772 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113717 none CC(=O)NC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 197, 197, 197, 197, 194, 194, 194, 78, 78, 78, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 78, 197, 197, 201, 201, 201, 201, 197, 197, 194, 78, 78, 78, 78, 13, 6, 6, 4, 4, 78, 78, 197] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 542 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113717 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113717/1 /scratch/stefan/7770410/working/building/REAL300020113717 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1046) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1046 `/scratch/stefan/7770410/working/3D/1046' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1) `REAL300020113717.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113717 none CC(=O)NC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 8, 8, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 47, 67, 77, 77, 77, 77, 13, 13, 1, 8, 8, 14, 14, 14, 14, 8, 8, 6, 1, 1, 1, 1, 13, 47, 47, 67, 67, 1, 1, 8] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47]) total number of confs: 326 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113717 none CC(=O)NC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 57, 57, 57, 57, 50, 50, 50, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 13, 57, 57, 89, 89, 89, 89, 57, 57, 50, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13, 57] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 307 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113717 none CC(=O)NC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 57, 57, 57, 139, 191, 197, 197, 197, 197, 57, 57, 8, 1, 1, 3, 3, 3, 3, 1, 1, 4, 8, 8, 8, 8, 57, 139, 139, 191, 191, 8, 8, 1] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 47, 27, 28] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 771 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113717 none CC(=O)NC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 197, 197, 197, 197, 194, 194, 194, 78, 78, 78, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 78, 197, 197, 201, 201, 201, 201, 197, 197, 194, 78, 78, 78, 78, 13, 6, 6, 4, 4, 78, 78, 197] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 542 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113717 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113717 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113717/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113717/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113717 Building REAL300020113718 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113718' /scratch/stefan/7770410/working/building/REAL300020113718 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113718 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113718/0 /scratch/stefan/7770410/working/building/REAL300020113718 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1047) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1047 `/scratch/stefan/7770410/working/3D/1047' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC(F)(F)C1) `REAL300020113718.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113718 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC(F)(F)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 15, 15, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 12, 12, 12, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 12, 41, 110, 110, 110, 110, 110, 110, 41, 12, 12, 12, 12, 1, 6, 6, 8, 8, 12, 12, 110, 110, 110, 110, 110, 110, 110] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 331 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113718 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC(F)(F)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 15, 15, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [129, 129, 60, 60, 60, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 60, 129, 201, 201, 201, 201, 201, 201, 129, 60, 60, 60, 60, 10, 6, 6, 4, 4, 60, 60, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 595 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113718 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC(F)(F)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 15, 15, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 33, 51, 60, 60, 60, 60, 12, 12, 1, 6, 29, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 12, 33, 33, 51, 51, 1, 1, 29, 29, 29, 29, 29, 29, 29] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113718 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC(F)(F)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 15, 15, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 29, 29, 29, 110, 110, 110, 179, 201, 201, 201, 201, 201, 110, 110, 29, 1, 1, 1, 1, 1, 1, 1, 8, 29, 29, 29, 29, 110, 179, 179, 201, 201, 29, 29, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 38, 39, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 646 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113718 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113718/1 /scratch/stefan/7770410/working/building/REAL300020113718 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1048) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1048 `/scratch/stefan/7770410/working/3D/1048' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC(F)(F)C1) `REAL300020113718.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113718/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113718 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC(F)(F)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 15, 15, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 12, 12, 12, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 12, 41, 110, 110, 110, 110, 110, 110, 41, 12, 12, 12, 12, 1, 6, 6, 8, 8, 12, 12, 110, 110, 110, 110, 110, 110, 110] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 331 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113718 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC(F)(F)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 15, 15, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 60, 60, 60, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 60, 128, 201, 201, 201, 201, 201, 201, 128, 60, 60, 60, 60, 10, 6, 6, 4, 4, 60, 60, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 595 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113718 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC(F)(F)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 15, 15, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 33, 51, 60, 60, 60, 60, 12, 12, 1, 6, 29, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 12, 33, 33, 51, 51, 1, 1, 29, 29, 29, 29, 29, 29, 29] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113718 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC(F)(F)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 15, 15, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 29, 29, 29, 110, 110, 110, 179, 201, 201, 201, 201, 201, 110, 110, 29, 1, 1, 1, 1, 1, 1, 1, 8, 29, 29, 29, 29, 110, 179, 179, 201, 201, 29, 29, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 38, 39, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 646 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113718 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113718 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113718/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113718/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113718 Building REAL300020113719 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113719' /scratch/stefan/7770410/working/building/REAL300020113719 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113719 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113719/0 /scratch/stefan/7770410/working/building/REAL300020113719 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1049) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1049 `/scratch/stefan/7770410/working/3D/1049' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(F)=C1) `REAL300020113719.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113719 none COC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 32, 32, 32, 32, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 38, 47, 63, 63, 63, 63, 7, 7, 1, 32, 32, 32, 47, 47, 47, 32, 6, 1, 1, 1, 1, 7, 38, 38, 47, 47, 1, 1, 32] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 278 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113719 none COC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 82, 82, 82, 82, 26, 26, 26, 7, 7, 7, 1, 1, 1, 1, 1, 9, 13, 19, 19, 19, 19, 1, 1, 7, 82, 82, 82, 109, 109, 109, 82, 26, 7, 7, 7, 7, 1, 9, 9, 13, 13, 7, 7, 82] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 259 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113719 none COC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 32, 32, 32, 82, 82, 82, 171, 188, 201, 201, 201, 201, 82, 82, 32, 1, 1, 1, 3, 3, 3, 1, 13, 32, 32, 32, 32, 82, 171, 171, 188, 188, 32, 32, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 44, 25, 26, 27, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 662 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113719 none COC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 154, 154, 154, 78, 78, 78, 30, 30, 30, 6, 4, 1, 1, 1, 1, 1, 1, 30, 30, 78, 201, 201, 201, 201, 201, 201, 201, 154, 78, 78, 78, 78, 30, 6, 6, 4, 4, 78, 78, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 513 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113719 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113719/1 /scratch/stefan/7770410/working/building/REAL300020113719 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1050) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1050 `/scratch/stefan/7770410/working/3D/1050' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(F)=C1) `REAL300020113719.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113719 none COC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 32, 32, 32, 32, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 39, 48, 64, 64, 64, 64, 7, 7, 1, 32, 32, 32, 47, 47, 47, 32, 6, 1, 1, 1, 1, 7, 39, 39, 48, 48, 1, 1, 32] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 281 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113719 none COC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 82, 82, 82, 82, 26, 26, 26, 7, 7, 7, 1, 1, 1, 1, 1, 9, 13, 19, 19, 19, 19, 1, 1, 7, 82, 82, 82, 110, 110, 110, 82, 26, 7, 7, 7, 7, 1, 9, 9, 13, 13, 7, 7, 82] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 261 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113719 none COC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 32, 32, 32, 82, 82, 82, 172, 189, 201, 201, 201, 201, 82, 82, 32, 1, 1, 1, 3, 3, 3, 1, 13, 32, 32, 32, 32, 82, 172, 172, 189, 189, 32, 32, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 44, 25, 26, 27, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 663 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113719 none COC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 153, 153, 153, 78, 78, 78, 29, 29, 29, 6, 4, 1, 1, 1, 1, 1, 1, 29, 29, 78, 201, 201, 201, 201, 201, 201, 201, 153, 78, 78, 78, 78, 29, 6, 6, 4, 4, 78, 78, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 511 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113719 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113719 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113719/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113719/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113719 Building REAL300020113720 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113720' /scratch/stefan/7770410/working/building/REAL300020113720 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113720 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113720/0 /scratch/stefan/7770410/working/building/REAL300020113720 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1051) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1051 `/scratch/stefan/7770410/working/3D/1051' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2SC=CC2=NC=N1) `REAL300020113720.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113720 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2SC=CC2=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 12, 46, 94, 94, 94, 94, 94, 94, 94, 94, 46, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 94, 94, 94] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 232 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113720 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2SC=CC2=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [170, 170, 92, 92, 92, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 92, 170, 201, 201, 201, 201, 201, 201, 201, 201, 170, 92, 92, 92, 92, 18, 6, 6, 4, 4, 92, 92, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 531 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113720 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2SC=CC2=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 53, 71, 91, 91, 91, 91, 12, 12, 1, 6, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 12, 53, 53, 71, 71, 1, 1, 17, 17, 17] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113720 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2SC=CC2=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 17, 17, 17, 94, 94, 94, 163, 201, 201, 201, 201, 201, 94, 94, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 17, 17, 17, 17, 94, 163, 163, 201, 201, 17, 17, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 734 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113720 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113720/1 /scratch/stefan/7770410/working/building/REAL300020113720 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1052) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1052 `/scratch/stefan/7770410/working/3D/1052' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2SC=CC2=NC=N1) `REAL300020113720.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113720/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113720 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2SC=CC2=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 12, 46, 94, 94, 94, 94, 94, 94, 94, 94, 46, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 94, 94, 94] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 232 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113720 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2SC=CC2=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [170, 170, 92, 92, 92, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 92, 170, 201, 201, 201, 201, 201, 201, 201, 201, 170, 92, 92, 92, 92, 18, 6, 6, 4, 4, 92, 92, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 531 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113720 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2SC=CC2=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 53, 71, 91, 91, 91, 91, 12, 12, 1, 6, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 12, 53, 53, 71, 71, 1, 1, 17, 17, 17] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113720 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2SC=CC2=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 17, 17, 17, 94, 94, 94, 163, 201, 201, 201, 201, 201, 94, 94, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 17, 17, 17, 17, 94, 163, 163, 201, 201, 17, 17, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 734 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113720 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113720 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113720/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113720/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113720 Building REAL300020113721 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113721' /scratch/stefan/7770410/working/building/REAL300020113721 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113721 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113721/0 /scratch/stefan/7770410/working/building/REAL300020113721 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1053) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1053 `/scratch/stefan/7770410/working/3D/1053' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)N1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=N1) `REAL300020113721.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113721 none CC(C)(C)N1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 30, 63, 63, 30, 30, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 40, 49, 68, 68, 68, 68, 7, 7, 1, 30, 30, 63, 63, 63, 63, 63, 63, 63, 63, 63, 30, 6, 1, 1, 1, 1, 7, 40, 40, 49, 49, 1, 1] 201 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 48, 49, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 408 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113721 none CC(C)(C)N1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 75, 114, 114, 75, 75, 23, 23, 23, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 17, 17, 17, 17, 1, 1, 7, 75, 75, 114, 114, 114, 114, 114, 114, 114, 114, 114, 75, 23, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7] 201 rigid atoms, others: [43, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 380 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113721 none CC(C)(C)N1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 13, 13, 13, 30, 30, 30, 75, 75, 75, 156, 183, 201, 201, 201, 201, 75, 75, 30, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 13, 30, 30, 30, 30, 75, 156, 156, 183, 183, 30, 30] 201 rigid atoms, others: [1, 4, 5, 6, 7, 26, 27, 37] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 703 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113721 none CC(C)(C)N1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 138, 138, 138, 79, 79, 79, 28, 28, 28, 7, 4, 1, 1, 1, 1, 1, 1, 28, 28, 79, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 138, 79, 79, 79, 79, 28, 7, 7, 4, 4, 79, 79] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 489 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113721 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113721/1 /scratch/stefan/7770410/working/building/REAL300020113721 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1054) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1054 `/scratch/stefan/7770410/working/3D/1054' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)N1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=N1) `REAL300020113721.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113721/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113721 none CC(C)(C)N1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 30, 63, 63, 30, 30, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 40, 49, 67, 67, 67, 67, 7, 7, 1, 30, 30, 63, 63, 63, 63, 63, 63, 63, 63, 63, 30, 6, 1, 1, 1, 1, 7, 40, 40, 49, 49, 1, 1] 201 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 48, 49, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 406 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113721 none CC(C)(C)N1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 74, 113, 113, 74, 74, 22, 22, 22, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 17, 17, 17, 17, 1, 1, 7, 74, 74, 113, 113, 113, 113, 113, 113, 113, 113, 113, 74, 22, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7] 201 rigid atoms, others: [43, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 378 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113721 none CC(C)(C)N1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 13, 13, 13, 30, 30, 30, 74, 74, 74, 156, 183, 201, 201, 201, 201, 74, 74, 30, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 13, 30, 30, 30, 30, 74, 156, 156, 183, 183, 30, 30] 201 rigid atoms, others: [1, 4, 5, 6, 7, 26, 27, 37] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 705 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113721 none CC(C)(C)N1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 137, 137, 137, 79, 79, 79, 29, 29, 29, 7, 4, 1, 1, 1, 1, 1, 1, 29, 29, 79, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 137, 79, 79, 79, 79, 29, 7, 7, 4, 4, 79, 79] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 490 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113721 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113721 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113721/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113721/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113721 Building REAL300020113722 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113722' /scratch/stefan/7770410/working/building/REAL300020113722 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113722 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113722/0 /scratch/stefan/7770410/working/building/REAL300020113722 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1055) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1055 `/scratch/stefan/7770410/working/3D/1055' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC=CN=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113722.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113722 none CC(=O)NC1=CC=CN=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 38, 56, 60, 60, 60, 60, 13, 13, 1, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 13, 38, 38, 56, 56, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 46, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 257 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113722 none CC(=O)NC1=CC=CN=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 73, 73, 73, 73, 73, 73, 56, 56, 56, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 73, 73, 73, 73, 73, 73, 73, 56, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 201 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113722 none CC(=O)NC1=CC=CN=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 73, 73, 73, 141, 201, 201, 201, 201, 201, 73, 73, 13, 4, 4, 4, 4, 1, 1, 1, 6, 13, 13, 13, 13, 73, 141, 141, 201, 201, 13, 13] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 35] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 812 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113722 none CC(=O)NC1=CC=CN=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 178, 178, 178, 62, 62, 62, 12, 12, 12, 7, 4, 1, 1, 1, 1, 1, 1, 12, 12, 62, 201, 201, 201, 201, 201, 201, 201, 178, 62, 62, 62, 62, 12, 7, 7, 4, 4, 62, 62] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 514 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113722 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113722/1 /scratch/stefan/7770410/working/building/REAL300020113722 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1056) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1056 `/scratch/stefan/7770410/working/3D/1056' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC=CN=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113722.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113722 none CC(=O)NC1=CC=CN=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 38, 56, 60, 60, 60, 60, 13, 13, 1, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 13, 38, 38, 56, 56, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 46, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 257 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113722 none CC(=O)NC1=CC=CN=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 73, 73, 73, 73, 73, 73, 56, 56, 56, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 73, 73, 73, 73, 73, 73, 73, 56, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 201 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113722 none CC(=O)NC1=CC=CN=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 73, 73, 73, 141, 201, 201, 201, 201, 201, 73, 73, 13, 4, 4, 4, 4, 1, 1, 1, 6, 13, 13, 13, 13, 73, 141, 141, 201, 201, 13, 13] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 35] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 812 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113722 none CC(=O)NC1=CC=CN=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 176, 176, 176, 59, 59, 59, 11, 11, 11, 7, 4, 1, 1, 1, 1, 1, 1, 11, 11, 59, 201, 201, 201, 201, 201, 201, 201, 176, 59, 59, 59, 59, 11, 7, 7, 4, 4, 59, 59] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 515 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113722 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113722 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113722/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113722/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113722 Building REAL300020113723 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113723' /scratch/stefan/7770410/working/building/REAL300020113723 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113723 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113723/0 /scratch/stefan/7770410/working/building/REAL300020113723 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1057) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1057 `/scratch/stefan/7770410/working/3D/1057' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=CC2=C1) `REAL300020113723.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113723 none CC1=CN2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 30, 45, 45, 45, 45, 45, 9, 9, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 9, 30, 30, 45, 45, 1, 1, 16, 16, 16] 201 rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 11, 12, 45, 44, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 212 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113723 none CC1=CN2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 72, 72, 26, 26, 26, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 9, 72, 72, 72, 72, 72, 72, 72, 72, 72, 26, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 72, 72, 72] 201 rigid atoms, others: [39, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 163 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113723 none CC1=CN2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 72, 72, 72, 145, 201, 201, 201, 201, 201, 72, 72, 16, 1, 1, 1, 1, 2, 2, 2, 1, 1, 5, 16, 16, 16, 16, 72, 145, 145, 201, 201, 16, 16, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 46, 47, 48, 25, 33, 27, 28, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 817 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113723 none CC1=CN2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 80, 80, 80, 45, 45, 45, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 45, 201, 201, 201, 201, 201, 201, 201, 201, 201, 80, 45, 45, 45, 45, 8, 4, 4, 2, 2, 45, 45, 201, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 407 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113723 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113723/1 /scratch/stefan/7770410/working/building/REAL300020113723 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1058) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1058 `/scratch/stefan/7770410/working/3D/1058' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=CC2=C1) `REAL300020113723.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113723 none CC1=CN2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 30, 45, 45, 45, 45, 45, 9, 9, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 9, 30, 30, 45, 45, 1, 1, 16, 16, 16] 201 rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 11, 12, 45, 44, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 212 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113723 none CC1=CN2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 72, 72, 26, 26, 26, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 9, 72, 72, 72, 72, 72, 72, 72, 72, 72, 26, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 72, 72, 72] 201 rigid atoms, others: [39, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 163 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113723 none CC1=CN2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 72, 72, 72, 145, 201, 201, 201, 201, 201, 72, 72, 16, 1, 1, 1, 1, 2, 2, 2, 1, 1, 5, 16, 16, 16, 16, 72, 145, 145, 201, 201, 16, 16, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 46, 47, 48, 25, 33, 27, 28, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 817 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113723 none CC1=CN2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 80, 80, 80, 45, 45, 45, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 45, 201, 201, 201, 201, 201, 201, 201, 201, 201, 80, 45, 45, 45, 45, 8, 4, 4, 2, 2, 45, 45, 201, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 407 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113723 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113723 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113723/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113723/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113723 Building REAL300020113724 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113724' /scratch/stefan/7770410/working/building/REAL300020113724 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113724 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113724/0 /scratch/stefan/7770410/working/building/REAL300020113724 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1059) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1059 `/scratch/stefan/7770410/working/3D/1059' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(F)CCOCC1) `REAL300020113724.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113724 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(F)CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 15, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 13, 13, 13, 1, 1, 1, 1, 1, 4, 6, 6, 6, 6, 6, 1, 1, 13, 57, 166, 166, 166, 166, 166, 166, 57, 13, 13, 13, 13, 1, 4, 4, 6, 6, 13, 13, 166, 166, 166, 166, 166, 166, 166, 166] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 485 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113724 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(F)CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 15, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 42, 42, 42, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 42, 115, 201, 201, 201, 201, 201, 201, 115, 42, 42, 42, 42, 7, 4, 4, 2, 2, 42, 42, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 594 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113724 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(F)CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 15, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 27, 41, 41, 41, 41, 41, 13, 13, 1, 6, 37, 37, 37, 37, 37, 37, 6, 1, 1, 1, 1, 13, 27, 27, 41, 41, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113724 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(F)CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 15, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 37, 37, 37, 166, 166, 166, 187, 201, 201, 201, 201, 201, 166, 166, 37, 1, 1, 1, 1, 1, 1, 1, 12, 37, 37, 37, 37, 166, 187, 187, 201, 201, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 38, 39, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 461 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113724 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113724/1 /scratch/stefan/7770410/working/building/REAL300020113724 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1060) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1060 `/scratch/stefan/7770410/working/3D/1060' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(F)CCOCC1) `REAL300020113724.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113724/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113724 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(F)CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 15, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 13, 57, 167, 167, 167, 167, 167, 167, 57, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 167, 167, 167, 167, 167, 167, 167, 167] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 490 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113724 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(F)CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 15, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 41, 41, 41, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 41, 115, 201, 201, 201, 201, 201, 201, 115, 41, 41, 41, 41, 7, 4, 4, 2, 2, 41, 41, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 593 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113724 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(F)CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 15, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 27, 41, 41, 41, 41, 41, 13, 13, 1, 6, 36, 36, 36, 36, 36, 36, 6, 1, 1, 1, 1, 13, 27, 27, 41, 41, 1, 1, 36, 36, 36, 36, 36, 36, 36, 36] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113724 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(F)CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 15, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 36, 36, 36, 167, 167, 167, 188, 201, 201, 201, 201, 201, 167, 167, 36, 1, 1, 1, 1, 1, 1, 1, 12, 36, 36, 36, 36, 167, 188, 188, 201, 201, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 38, 39, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 455 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113724 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113724 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113724/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113724/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113724 Building REAL300020113725 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113725' /scratch/stefan/7770410/working/building/REAL300020113725 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113725 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113725/0 /scratch/stefan/7770410/working/building/REAL300020113725 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1061) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1061 `/scratch/stefan/7770410/working/3D/1061' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CNC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113725.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113725 none O=C(CCC1=CNC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 20, 20, 28, 28, 28, 28, 1, 1, 1, 1, 1, 11, 11, 11, 33, 47, 50, 50, 50, 50, 11, 11, 1, 20, 20, 20, 20, 28, 28, 28, 6, 1, 1, 1, 1, 11, 33, 33, 47, 47, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 280 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113725 none O=C(CCC1=CNC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 97, 97, 118, 118, 118, 118, 11, 11, 11, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 11, 97, 97, 97, 97, 118, 118, 118, 38, 11, 11, 11, 11, 1, 5, 5, 7, 7, 11, 11] 201 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 426 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113725 none O=C(CCC1=CNC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 5, 1, 1, 1, 1, 1, 1, 9, 9, 28, 28, 28, 118, 118, 118, 179, 201, 201, 201, 201, 201, 118, 118, 28, 5, 5, 5, 5, 1, 1, 1, 9, 28, 28, 28, 28, 118, 179, 179, 201, 201, 28, 28] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 643 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113725 none O=C(CCC1=CNC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 109, 201, 201, 201, 201, 201, 201, 49, 49, 49, 9, 9, 9, 6, 4, 1, 1, 1, 1, 1, 1, 9, 9, 49, 201, 201, 201, 201, 201, 201, 201, 109, 49, 49, 49, 49, 9, 6, 6, 4, 4, 49, 49] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 730 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113725 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113725/1 /scratch/stefan/7770410/working/building/REAL300020113725 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1062) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1062 `/scratch/stefan/7770410/working/3D/1062' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CNC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113725.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113725 none O=C(CCC1=CNC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 20, 20, 28, 28, 28, 28, 1, 1, 1, 1, 1, 11, 11, 11, 33, 47, 50, 50, 50, 50, 11, 11, 1, 20, 20, 20, 20, 28, 28, 28, 6, 1, 1, 1, 1, 11, 33, 33, 47, 47, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 280 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113725 none O=C(CCC1=CNC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 96, 96, 117, 117, 117, 117, 11, 11, 11, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 11, 96, 96, 96, 96, 117, 117, 117, 38, 11, 11, 11, 11, 1, 5, 5, 7, 7, 11, 11] 201 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 420 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113725 none O=C(CCC1=CNC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 5, 1, 1, 1, 1, 1, 1, 9, 9, 28, 28, 28, 117, 117, 117, 179, 201, 201, 201, 201, 201, 117, 117, 28, 5, 5, 5, 5, 1, 1, 1, 9, 28, 28, 28, 28, 117, 179, 179, 201, 201, 28, 28] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 645 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113725 none O=C(CCC1=CNC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 109, 201, 201, 201, 201, 201, 201, 49, 49, 49, 9, 9, 9, 6, 4, 1, 1, 1, 1, 1, 1, 9, 9, 49, 201, 201, 201, 201, 201, 201, 201, 109, 49, 49, 49, 49, 9, 6, 6, 4, 4, 49, 49] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 730 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113725 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113725 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113725/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113725/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113725 Building REAL300020113726 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113726' /scratch/stefan/7770410/working/building/REAL300020113726 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113726 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113726/0 /scratch/stefan/7770410/working/building/REAL300020113726 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1063) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1063 `/scratch/stefan/7770410/working/3D/1063' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCC(F)(F)C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113726.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113726 none O=C(CC1CCC(F)(F)C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 15, 15, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 42, 73, 73, 73, 73, 73, 73, 1, 1, 1, 1, 1, 13, 13, 13, 14, 15, 15, 15, 15, 15, 13, 13, 1, 42, 42, 73, 73, 73, 73, 73, 73, 73, 6, 1, 1, 1, 1, 13, 14, 14, 15, 15, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 279 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113726 none O=C(CC1CCC(F)(F)C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 15, 15, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 165, 201, 201, 201, 201, 201, 201, 13, 13, 13, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 1, 1, 13, 165, 165, 201, 201, 201, 201, 201, 201, 201, 45, 13, 13, 13, 13, 1, 3, 3, 4, 4, 13, 13] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 745 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113726 none O=C(CC1CCC(F)(F)C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 15, 15, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 6, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 73, 73, 73, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 73, 6, 6, 1, 1, 1, 1, 1, 1, 1, 25, 73, 73, 73, 73, 201, 201, 201, 201, 201, 73, 73] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 378 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113726 none O=C(CC1CCC(F)(F)C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 15, 15, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 167, 201, 201, 201, 201, 201, 201, 15, 15, 15, 4, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 4, 4, 15, 167, 167, 201, 201, 201, 201, 201, 201, 201, 47, 15, 15, 15, 15, 4, 4, 4, 2, 2, 15, 15] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 739 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113726 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113726/1 /scratch/stefan/7770410/working/building/REAL300020113726 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1064) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1064 `/scratch/stefan/7770410/working/3D/1064' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCC(F)(F)C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113726.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113726/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113726 none O=C(CC1CCC(F)(F)C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 15, 15, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 42, 73, 73, 73, 73, 73, 73, 1, 1, 1, 1, 1, 13, 13, 13, 14, 14, 14, 14, 14, 14, 13, 13, 1, 42, 42, 73, 73, 73, 73, 73, 73, 73, 6, 1, 1, 1, 1, 13, 14, 14, 14, 14, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 273 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113726 none O=C(CC1CCC(F)(F)C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 15, 15, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 165, 201, 201, 201, 201, 201, 201, 13, 13, 13, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 13, 165, 165, 201, 201, 201, 201, 201, 201, 201, 45, 13, 13, 13, 13, 1, 3, 3, 3, 3, 13, 13] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 736 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113726 none O=C(CC1CCC(F)(F)C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 15, 15, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 6, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 73, 73, 73, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 73, 6, 6, 1, 1, 1, 1, 1, 1, 1, 25, 73, 73, 73, 73, 201, 201, 201, 201, 201, 73, 73] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 378 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113726 none O=C(CC1CCC(F)(F)C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 15, 15, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 167, 201, 201, 201, 201, 201, 201, 15, 15, 15, 4, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 4, 4, 15, 167, 167, 201, 201, 201, 201, 201, 201, 201, 47, 15, 15, 15, 15, 4, 4, 4, 2, 2, 15, 15] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 739 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113726 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113726 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113726/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113726/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113726 Building REAL300020113727 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113727' /scratch/stefan/7770410/working/building/REAL300020113727 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113727 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113727/0 /scratch/stefan/7770410/working/building/REAL300020113727 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1065) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1065 `/scratch/stefan/7770410/working/3D/1065' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1(C2=CC=CC=C2)CC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113727.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113727 none O=C(CC1(C2=CC=CC=C2)CC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 13, 40, 40, 40, 147, 147, 147, 187, 201, 201, 201, 201, 201, 147, 147, 40, 6, 6, 1, 1, 1, 1, 1, 3, 3, 3, 3, 13, 40, 40, 40, 40, 147, 187, 187, 201, 201, 40, 40] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 35, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 554 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113727 none O=C(CC1(C2=CC=CC=C2)CC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 120, 195, 201, 201, 201, 201, 201, 201, 201, 201, 45, 45, 45, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 45, 195, 195, 201, 201, 201, 201, 201, 201, 201, 201, 201, 120, 45, 45, 45, 45, 8, 4, 4, 2, 2, 45, 45] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 711 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113727 none O=C(CC1(C2=CC=CC=C2)CC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 28, 38, 40, 40, 38, 40, 40, 38, 38, 1, 1, 1, 1, 1, 13, 13, 13, 31, 43, 43, 43, 43, 43, 13, 13, 1, 28, 28, 40, 40, 40, 40, 40, 38, 38, 38, 38, 6, 1, 1, 1, 1, 13, 31, 31, 43, 43, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 312 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113727 none O=C(CC1(C2=CC=CC=C2)CC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 4, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 12, 12, 38, 38, 38, 145, 145, 145, 185, 201, 201, 201, 201, 201, 145, 145, 38, 4, 4, 3, 3, 3, 3, 3, 1, 1, 1, 1, 12, 38, 38, 38, 38, 145, 185, 185, 201, 201, 38, 38] 201 rigid atoms, others: [2, 3, 36, 37, 38, 39, 10, 11, 4] set([0, 1, 5, 6, 7, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 564 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113727 none O=C(CC1(C2=CC=CC=C2)CC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 125, 145, 147, 147, 145, 147, 147, 145, 145, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 125, 125, 147, 147, 147, 147, 147, 145, 145, 145, 145, 52, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 582 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113727 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113727/1 /scratch/stefan/7770410/working/building/REAL300020113727 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1066) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1066 `/scratch/stefan/7770410/working/3D/1066' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1(C2=CC=CC=C2)CC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113727.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113727/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113727 none O=C(CC1(C2=CC=CC=C2)CC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 13, 40, 40, 40, 147, 147, 147, 188, 201, 201, 201, 201, 201, 147, 147, 40, 6, 6, 1, 1, 1, 1, 1, 3, 3, 3, 3, 13, 40, 40, 40, 40, 147, 188, 188, 201, 201, 40, 40] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 35, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 554 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113727 none O=C(CC1(C2=CC=CC=C2)CC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 120, 195, 201, 201, 201, 201, 201, 201, 201, 201, 45, 45, 45, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 45, 195, 195, 201, 201, 201, 201, 201, 201, 201, 201, 201, 120, 45, 45, 45, 45, 8, 4, 4, 2, 2, 45, 45] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 713 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113727 none O=C(CC1(C2=CC=CC=C2)CC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 28, 38, 40, 40, 38, 40, 40, 38, 38, 1, 1, 1, 1, 1, 13, 13, 13, 32, 44, 44, 44, 44, 44, 13, 13, 1, 28, 28, 40, 40, 40, 40, 40, 38, 38, 38, 38, 6, 1, 1, 1, 1, 13, 32, 32, 44, 44, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 315 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113727 none O=C(CC1(C2=CC=CC=C2)CC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 4, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 12, 12, 38, 38, 38, 145, 145, 145, 186, 201, 201, 201, 201, 201, 145, 145, 38, 4, 4, 3, 3, 3, 3, 3, 1, 1, 1, 1, 12, 38, 38, 38, 38, 145, 186, 186, 201, 201, 38, 38] 201 rigid atoms, others: [2, 3, 36, 37, 38, 39, 10, 11, 4] set([0, 1, 5, 6, 7, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 564 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113727 none O=C(CC1(C2=CC=CC=C2)CC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 125, 145, 147, 147, 145, 147, 147, 145, 145, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 125, 125, 147, 147, 147, 147, 147, 145, 145, 145, 145, 52, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 582 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113727 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113727 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113727/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113727/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113727 Building REAL300020113728 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113728' /scratch/stefan/7770410/working/building/REAL300020113728 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113728 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113728/0 /scratch/stefan/7770410/working/building/REAL300020113728 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1067) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1067 `/scratch/stefan/7770410/working/3D/1067' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(C(F)F)N=C1) `REAL300020113728.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113728 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(C(F)F)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 15, 15, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 28, 70, 70, 70, 70, 114, 114, 70, 70, 28, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 70, 70, 114, 70] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 416 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113728 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(C(F)F)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 15, 15, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 50, 50, 50, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 50, 93, 201, 201, 201, 201, 201, 201, 201, 201, 93, 50, 50, 50, 50, 11, 6, 6, 4, 4, 50, 50, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 430 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113728 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(C(F)F)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 15, 15, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 32, 47, 50, 50, 50, 50, 11, 11, 1, 6, 13, 13, 13, 13, 30, 30, 13, 13, 6, 1, 1, 1, 1, 11, 32, 32, 47, 47, 1, 1, 13, 13, 30, 13] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 298 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113728 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(C(F)F)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 15, 15, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 13, 13, 13, 70, 70, 70, 145, 199, 201, 201, 201, 201, 70, 70, 13, 1, 1, 1, 1, 1, 5, 5, 1, 1, 5, 13, 13, 13, 13, 70, 145, 145, 199, 199, 13, 13, 1, 1, 5, 1] 201 rigid atoms, others: [1, 40, 41, 43, 19, 20, 21, 22, 23, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 812 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113728 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113728/1 /scratch/stefan/7770410/working/building/REAL300020113728 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1068) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1068 `/scratch/stefan/7770410/working/3D/1068' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(C(F)F)N=C1) `REAL300020113728.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113728 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(C(F)F)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 15, 15, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 28, 70, 70, 70, 70, 113, 113, 70, 70, 28, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 70, 70, 113, 70] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 413 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113728 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(C(F)F)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 15, 15, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 51, 51, 51, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 51, 94, 201, 201, 201, 201, 201, 201, 201, 201, 94, 51, 51, 51, 51, 12, 6, 6, 4, 4, 51, 51, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 431 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113728 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(C(F)F)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 15, 15, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 48, 51, 51, 51, 51, 11, 11, 1, 6, 13, 13, 13, 13, 30, 30, 13, 13, 6, 1, 1, 1, 1, 11, 33, 33, 48, 48, 1, 1, 13, 13, 30, 13] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113728 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(C(F)F)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 15, 15, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 13, 13, 13, 70, 70, 70, 145, 199, 201, 201, 201, 201, 70, 70, 13, 1, 1, 1, 1, 1, 5, 5, 1, 1, 5, 13, 13, 13, 13, 70, 145, 145, 199, 199, 13, 13, 1, 1, 5, 1] 201 rigid atoms, others: [1, 40, 41, 43, 19, 20, 21, 22, 23, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 812 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113728 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113728 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113728/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113728/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113728 Building REAL300020113729 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113729' /scratch/stefan/7770410/working/building/REAL300020113729 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113729 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113729/0 /scratch/stefan/7770410/working/building/REAL300020113729 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1069) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1069 `/scratch/stefan/7770410/working/3D/1069' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCN1C=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113729.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113729 none C=CCN1C=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 22, 11, 11, 11, 11, 11, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 22, 34, 34, 34, 34, 34, 8, 8, 1, 37, 37, 37, 22, 22, 11, 11, 11, 5, 1, 1, 1, 1, 8, 22, 22, 34, 34, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 271 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113729 none C=CCN1C=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 88, 46, 46, 46, 46, 46, 19, 19, 19, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 111, 111, 111, 88, 88, 46, 46, 46, 19, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 454 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113729 none C=CCN1C=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 46, 46, 46, 98, 131, 131, 131, 131, 131, 46, 46, 11, 10, 10, 10, 5, 5, 1, 1, 1, 4, 11, 11, 11, 11, 46, 98, 98, 131, 131, 11, 11] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 567 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113729 none C=CCN1C=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 132, 132, 132, 132, 132, 62, 62, 62, 34, 34, 34, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 34, 201, 201, 201, 201, 201, 132, 132, 132, 62, 34, 34, 34, 34, 8, 4, 4, 2, 2, 34, 34] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 701 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113729 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113729/1 /scratch/stefan/7770410/working/building/REAL300020113729 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1070) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1070 `/scratch/stefan/7770410/working/3D/1070' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCN1C=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113729.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113729 none C=CCN1C=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 22, 11, 11, 11, 11, 11, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 21, 33, 33, 33, 33, 33, 7, 7, 1, 37, 37, 37, 22, 22, 11, 11, 11, 5, 1, 1, 1, 1, 7, 21, 21, 33, 33, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 270 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113729 none C=CCN1C=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 86, 45, 45, 45, 45, 45, 18, 18, 18, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 109, 109, 109, 86, 86, 45, 45, 45, 18, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 449 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113729 none C=CCN1C=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 45, 45, 45, 98, 131, 131, 131, 131, 131, 45, 45, 11, 10, 10, 10, 5, 5, 1, 1, 1, 4, 11, 11, 11, 11, 45, 98, 98, 131, 131, 11, 11] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 569 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113729 none C=CCN1C=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 132, 132, 132, 132, 132, 63, 63, 63, 35, 35, 35, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 35, 201, 201, 201, 201, 201, 132, 132, 132, 63, 35, 35, 35, 35, 9, 4, 4, 2, 2, 35, 35] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 702 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113729 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113729 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113729/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113729/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113729 Building REAL300020113730 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113730' /scratch/stefan/7770410/working/building/REAL300020113730 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113730 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113730/0 /scratch/stefan/7770410/working/building/REAL300020113730 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1071) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1071 `/scratch/stefan/7770410/working/3D/1071' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CC=NC=C2S1) `REAL300020113730.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113730 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CC=NC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 12, 50, 101, 101, 101, 101, 101, 101, 101, 101, 50, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 101, 101, 101, 101] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 248 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113730 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CC=NC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [155, 155, 86, 86, 86, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 86, 155, 201, 201, 201, 201, 201, 201, 201, 201, 155, 86, 86, 86, 86, 17, 6, 6, 4, 4, 86, 86, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 508 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113730 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CC=NC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 49, 68, 84, 84, 84, 84, 12, 12, 1, 6, 24, 24, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 12, 49, 49, 68, 68, 1, 1, 24, 24, 24, 24] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 337 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113730 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CC=NC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 24, 24, 24, 101, 101, 101, 156, 201, 201, 201, 201, 201, 101, 101, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 24, 24, 24, 24, 101, 156, 156, 201, 201, 24, 24, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 700 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113730 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113730/1 /scratch/stefan/7770410/working/building/REAL300020113730 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1072) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1072 `/scratch/stefan/7770410/working/3D/1072' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CC=NC=C2S1) `REAL300020113730.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113730/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113730 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CC=NC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 12, 50, 99, 99, 99, 99, 99, 99, 99, 99, 50, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 99, 99, 99, 99] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 245 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113730 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CC=NC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 88, 88, 88, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 88, 156, 201, 201, 201, 201, 201, 201, 201, 201, 156, 88, 88, 88, 88, 17, 6, 6, 4, 4, 88, 88, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 510 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113730 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CC=NC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 51, 70, 86, 86, 86, 86, 12, 12, 1, 6, 25, 25, 25, 25, 25, 25, 25, 25, 6, 1, 1, 1, 1, 12, 51, 51, 70, 70, 1, 1, 25, 25, 25, 25] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113730 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CC=NC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 25, 25, 25, 99, 99, 99, 157, 201, 201, 201, 201, 201, 99, 99, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 25, 25, 25, 25, 99, 157, 157, 201, 201, 25, 25, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 707 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113730 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113730 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113730/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113730/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113730 Building REAL300020113731 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113731' /scratch/stefan/7770410/working/building/REAL300020113731 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300020113731 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113731/0 /scratch/stefan/7770410/working/building/REAL300020113731 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1073) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1073 `/scratch/stefan/7770410/working/3D/1073' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@H+](CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC1) `REAL300020113731.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113731 none C[N@H+](CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [52, 48, 52, 27, 27, 27, 9, 9, 9, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 9, 52, 52, 52, 52, 52, 52, 52, 48, 48, 27, 9, 9, 9, 9, 1, 3, 3, 3, 3, 9, 9, 52, 52, 52, 52, 52, 52, 52] 52 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 206 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113731 none C[N@H+](CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [48, 44, 48, 27, 27, 27, 9, 9, 9, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 48, 48, 48, 48, 48, 48, 48, 44, 44, 27, 9, 9, 9, 9, 3, 3, 3, 1, 1, 9, 9, 48, 48, 48, 48, 48, 48, 48] 48 rigid atoms, others: [40, 41, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 186 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113731 none C[N@H+](CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [23, 20, 23, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 23, 24, 24, 24, 23, 23, 23, 20, 20, 6, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 24, 24, 24, 24, 24, 24, 24] 52 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113731 none C[N@H+](CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 5, 14, 14, 14, 24, 24, 24, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 24, 1, 1, 1, 1, 3, 3, 3, 5, 5, 14, 24, 24, 24, 24, 52, 52, 52, 52, 52, 24, 24, 1, 1, 1, 1, 1, 1, 1] 52 rigid atoms, others: [1, 44, 45, 46, 47, 48, 49, 50, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 123 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113731 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113731/1 /scratch/stefan/7770410/working/building/REAL300020113731 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1074) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1074 `/scratch/stefan/7770410/working/3D/1074' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@@H+](CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC1) `REAL300020113731.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113731/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113731 none C[N@@H+](CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [62, 58, 62, 32, 32, 32, 10, 10, 10, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 10, 62, 62, 62, 62, 62, 62, 62, 58, 58, 32, 10, 10, 10, 10, 1, 4, 4, 4, 4, 10, 10, 62, 62, 62, 62, 62, 62, 62] 63 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 245 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113731 none C[N@@H+](CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 50, 53, 30, 30, 30, 11, 11, 11, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 53, 53, 53, 53, 53, 53, 53, 50, 50, 30, 11, 11, 11, 11, 4, 3, 3, 1, 1, 11, 11, 53, 53, 53, 53, 53, 53, 53] 53 rigid atoms, others: [40, 41, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 209 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113731 none C[N@@H+](CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [27, 22, 27, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 11, 11, 11, 11, 11, 11, 10, 10, 1, 27, 31, 31, 31, 27, 27, 27, 22, 22, 6, 1, 1, 1, 1, 10, 11, 11, 11, 11, 1, 1, 31, 31, 31, 31, 31, 31, 31] 63 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113731 none C[N@@H+](CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 8, 19, 19, 19, 31, 31, 31, 62, 62, 62, 63, 63, 63, 63, 63, 63, 62, 62, 31, 1, 1, 1, 1, 4, 4, 4, 8, 8, 19, 31, 31, 31, 31, 62, 63, 63, 63, 63, 31, 31, 1, 1, 1, 1, 1, 1, 1] 63 rigid atoms, others: [1, 44, 45, 46, 47, 48, 49, 50, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 147 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113731 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `2' /scratch/stefan/7770410/working/building/REAL300020113731/2 /scratch/stefan/7770410/working/building/REAL300020113731 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 2 (index: 1075) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1075 `/scratch/stefan/7770410/working/3D/1075' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC1) `REAL300020113731.mol2' -> `2.mol2' `temp.mol2' -> `REAL300020113731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113731/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113731 none CN(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 90, 41, 41, 41, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 14, 14, 14, 14, 1, 1, 11, 96, 109, 109, 109, 96, 96, 96, 90, 90, 41, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 109, 109, 109, 109, 109, 109, 109] 201 rigid atoms, others: [36, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 443 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113731 none CN(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 152, 152, 152, 75, 75, 75, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 75, 201, 201, 201, 201, 201, 201, 201, 201, 201, 152, 75, 75, 75, 75, 14, 6, 6, 4, 4, 75, 75, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 684 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113731 none CN(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 19, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 47, 64, 76, 76, 76, 76, 11, 11, 1, 22, 30, 30, 30, 22, 22, 22, 19, 19, 6, 1, 1, 1, 1, 11, 47, 47, 64, 64, 1, 1, 30, 30, 30, 30, 30, 30, 30] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 42, 21, 41] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 386 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113731 none CN(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 6, 12, 12, 12, 30, 30, 30, 109, 109, 109, 172, 201, 201, 201, 201, 201, 109, 109, 30, 1, 1, 1, 1, 3, 3, 3, 6, 6, 12, 30, 30, 30, 30, 109, 172, 172, 201, 201, 30, 30, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 43, 44, 45, 46, 47, 48, 49, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 694 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113731 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113731 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 2: /scratch/stefan/7770410/working/building/REAL300020113731/2.* 1: /scratch/stefan/7770410/working/building/REAL300020113731/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113731/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113731 Building REAL300020113732 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113732' /scratch/stefan/7770410/working/building/REAL300020113732 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113732 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113732/0 /scratch/stefan/7770410/working/building/REAL300020113732 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1076) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1076 `/scratch/stefan/7770410/working/3D/1076' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C(F)(F)F)N=CN1) `REAL300020113732.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113732 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C(F)(F)F)N=CN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 15, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 5, 11, 15, 15, 15, 15, 15, 15, 15, 15, 11, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 5, 15, 15] 16 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 50 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113732 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C(F)(F)F)N=CN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 15, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 8, 8, 8, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 8, 14, 16, 16, 16, 16, 16, 16, 16, 16, 14, 8, 8, 8, 8, 7, 4, 4, 2, 2, 8, 8, 16, 16] 16 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 48 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113732 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C(F)(F)F)N=CN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 15, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 5, 5, 1, 6, 14, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 14, 14] 16 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113732 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C(F)(F)F)N=CN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 15, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 14, 14, 14, 15, 15, 15, 16, 16, 16, 16, 16, 16, 15, 15, 14, 1, 1, 1, 2, 2, 2, 1, 1, 1, 7, 14, 14, 14, 14, 15, 16, 16, 16, 16, 14, 14, 1, 1] 16 rigid atoms, others: [1, 40, 41, 19, 20, 21, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 51 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113732 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113732/1 /scratch/stefan/7770410/working/building/REAL300020113732 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1077) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1077 `/scratch/stefan/7770410/working/3D/1077' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C(F)(F)F)N=CN1) `REAL300020113732.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113732 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C(F)(F)F)N=CN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 15, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 5, 11, 15, 15, 15, 15, 15, 15, 15, 15, 11, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 5, 15, 15] 16 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 50 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113732 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C(F)(F)F)N=CN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 15, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 8, 8, 8, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 8, 14, 16, 16, 16, 16, 16, 16, 16, 16, 14, 8, 8, 8, 8, 7, 4, 4, 2, 2, 8, 8, 16, 16] 16 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 48 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113732 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C(F)(F)F)N=CN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 15, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 5, 5, 1, 6, 14, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 14, 14] 16 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113732 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C(F)(F)F)N=CN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 15, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 14, 14, 14, 15, 15, 15, 16, 16, 16, 16, 16, 16, 15, 15, 14, 1, 1, 1, 2, 2, 2, 1, 1, 1, 7, 14, 14, 14, 14, 15, 16, 16, 16, 16, 14, 14, 1, 1] 16 rigid atoms, others: [1, 40, 41, 19, 20, 21, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 51 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113732 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113732 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113732/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113732/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113732 Building REAL300020113733 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113733' /scratch/stefan/7770410/working/building/REAL300020113733 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113733 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113733/0 /scratch/stefan/7770410/working/building/REAL300020113733 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1078) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1078 `/scratch/stefan/7770410/working/3D/1078' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C2OC=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C2=CC=C1) `REAL300020113733.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113733 none CC1=C2OC=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 48, 54, 54, 54, 54, 11, 11, 1, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 33, 33, 48, 48, 1, 1, 22, 22, 22] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 236 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113733 none CC1=C2OC=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 95, 95, 33, 33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 95, 95, 95, 95, 95, 95, 95, 95, 33, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 95, 95, 95] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 204 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113733 none CC1=C2OC=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 22, 22, 22, 95, 95, 95, 157, 201, 201, 201, 201, 201, 95, 95, 22, 1, 1, 1, 1, 2, 2, 2, 1, 8, 22, 22, 22, 22, 95, 157, 157, 201, 201, 22, 22, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 45, 46, 47, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 739 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113733 none CC1=C2OC=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 115, 115, 115, 55, 55, 55, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 55, 201, 201, 201, 201, 201, 201, 201, 201, 115, 55, 55, 55, 55, 11, 6, 6, 4, 4, 55, 55, 201, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 467 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113733 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113733/1 /scratch/stefan/7770410/working/building/REAL300020113733 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1079) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1079 `/scratch/stefan/7770410/working/3D/1079' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C2OC=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C2=CC=C1) `REAL300020113733.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113733/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113733 none CC1=C2OC=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 48, 54, 54, 54, 54, 11, 11, 1, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 33, 33, 48, 48, 1, 1, 22, 22, 22] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 236 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113733 none CC1=C2OC=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 94, 94, 33, 33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 94, 94, 94, 94, 94, 94, 94, 94, 33, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 94, 94, 94] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 203 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113733 none CC1=C2OC=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 22, 22, 22, 94, 94, 94, 157, 201, 201, 201, 201, 201, 94, 94, 22, 1, 1, 1, 1, 2, 2, 2, 1, 8, 22, 22, 22, 22, 94, 157, 157, 201, 201, 22, 22, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 45, 46, 47, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 741 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113733 none CC1=C2OC=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 116, 116, 116, 56, 56, 56, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 56, 201, 201, 201, 201, 201, 201, 201, 201, 116, 56, 56, 56, 56, 12, 6, 6, 4, 4, 56, 56, 201, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 466 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113733 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113733 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113733/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113733/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113733 Building REAL300020113734 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113734' /scratch/stefan/7770410/working/building/REAL300020113734 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113734 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113734/0 /scratch/stefan/7770410/working/building/REAL300020113734 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1080) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1080 `/scratch/stefan/7770410/working/3D/1080' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC2=CC=CN=C2S1) `REAL300020113734.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113734 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC2=CC=CN=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 1, 1, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 8, 8, 8, 1, 1, 1, 1, 1, 9, 13, 19, 19, 19, 19, 1, 1, 8, 31, 78, 78, 78, 78, 78, 78, 78, 78, 31, 8, 8, 8, 8, 1, 9, 9, 13, 13, 8, 8, 78, 78, 78] 163 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 209 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113734 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC2=CC=CN=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 1, 1, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [138, 138, 77, 77, 77, 28, 28, 28, 7, 4, 1, 1, 1, 1, 1, 1, 28, 28, 77, 138, 163, 163, 163, 163, 163, 163, 163, 163, 138, 77, 77, 77, 77, 28, 7, 7, 4, 4, 77, 77, 163, 163, 163] 163 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 433 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113734 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC2=CC=CN=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 1, 1, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 39, 52, 69, 69, 69, 69, 8, 8, 1, 6, 29, 29, 29, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 8, 39, 39, 52, 52, 1, 1, 29, 29, 29] 163 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113734 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC2=CC=CN=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 1, 1, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 29, 29, 29, 78, 78, 78, 138, 163, 163, 163, 163, 163, 78, 78, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 29, 29, 29, 29, 78, 138, 138, 163, 163, 29, 29, 1, 1, 1] 163 rigid atoms, others: [1, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 573 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113734 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113734/1 /scratch/stefan/7770410/working/building/REAL300020113734 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1081) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1081 `/scratch/stefan/7770410/working/3D/1081' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC2=CC=CN=C2S1) `REAL300020113734.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113734 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC2=CC=CN=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 1, 1, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 8, 8, 8, 1, 1, 1, 1, 1, 9, 13, 19, 19, 19, 19, 1, 1, 8, 31, 78, 78, 78, 78, 78, 78, 78, 78, 31, 8, 8, 8, 8, 1, 9, 9, 13, 13, 8, 8, 78, 78, 78] 163 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 209 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113734 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC2=CC=CN=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 1, 1, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [138, 138, 77, 77, 77, 28, 28, 28, 7, 4, 1, 1, 1, 1, 1, 1, 28, 28, 77, 138, 163, 163, 163, 163, 163, 163, 163, 163, 138, 77, 77, 77, 77, 28, 7, 7, 4, 4, 77, 77, 163, 163, 163] 163 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 433 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113734 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC2=CC=CN=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 1, 1, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 39, 52, 69, 69, 69, 69, 8, 8, 1, 6, 29, 29, 29, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 8, 39, 39, 52, 52, 1, 1, 29, 29, 29] 163 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113734 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC2=CC=CN=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 1, 1, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 29, 29, 29, 78, 78, 78, 138, 163, 163, 163, 163, 163, 78, 78, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 29, 29, 29, 29, 78, 138, 138, 163, 163, 29, 29, 1, 1, 1] 163 rigid atoms, others: [1, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 573 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113734 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113734 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113734/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113734/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113734 Building REAL300020113735 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113735' /scratch/stefan/7770410/working/building/REAL300020113735 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113735 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113735/0 /scratch/stefan/7770410/working/building/REAL300020113735 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1082) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1082 `/scratch/stefan/7770410/working/3D/1082' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=NC=CN2N=C1) `REAL300020113735.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113735 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=NC=CN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 5, 5, 5, 1, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 1, 1, 5, 17, 32, 32, 32, 32, 32, 32, 32, 32, 17, 5, 5, 5, 5, 1, 8, 8, 10, 10, 5, 5, 32, 32, 32, 32] 56 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113735 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=NC=CN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 25, 25, 25, 10, 10, 10, 4, 2, 1, 1, 1, 1, 1, 1, 10, 10, 25, 46, 56, 56, 56, 56, 56, 56, 56, 56, 46, 25, 25, 25, 25, 10, 4, 4, 2, 2, 25, 25, 56, 56, 56, 56] 56 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 150 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113735 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=NC=CN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 17, 25, 25, 25, 25, 25, 5, 5, 1, 6, 21, 21, 21, 21, 21, 21, 21, 20, 6, 1, 1, 1, 1, 5, 17, 17, 25, 25, 1, 1, 21, 21, 21, 21] 56 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113735 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=NC=CN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 21, 21, 21, 32, 32, 32, 48, 56, 56, 56, 56, 56, 32, 32, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 21, 21, 21, 21, 32, 48, 48, 56, 56, 21, 21, 1, 1, 1, 1] 56 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 198 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113735 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113735/1 /scratch/stefan/7770410/working/building/REAL300020113735 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1083) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1083 `/scratch/stefan/7770410/working/3D/1083' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=NC=CN2N=C1) `REAL300020113735.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113735/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113735 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=NC=CN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 5, 5, 5, 1, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 1, 1, 5, 17, 32, 32, 32, 32, 32, 32, 32, 32, 17, 5, 5, 5, 5, 1, 8, 8, 10, 10, 5, 5, 32, 32, 32, 32] 56 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113735 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=NC=CN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 25, 25, 25, 10, 10, 10, 4, 2, 1, 1, 1, 1, 1, 1, 10, 10, 25, 46, 56, 56, 56, 56, 56, 56, 56, 56, 46, 25, 25, 25, 25, 10, 4, 4, 2, 2, 25, 25, 56, 56, 56, 56] 56 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 150 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113735 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=NC=CN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 17, 25, 25, 25, 25, 25, 5, 5, 1, 6, 21, 21, 21, 21, 21, 21, 21, 20, 6, 1, 1, 1, 1, 5, 17, 17, 25, 25, 1, 1, 21, 21, 21, 21] 56 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113735 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=NC=CN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 21, 21, 21, 32, 32, 32, 48, 56, 56, 56, 56, 56, 32, 32, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 21, 21, 21, 21, 32, 48, 48, 56, 56, 21, 21, 1, 1, 1, 1] 56 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 198 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113735 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113735 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113735/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113735/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113735 Building REAL300020113736 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113736' /scratch/stefan/7770410/working/building/REAL300020113736 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113736 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113736/0 /scratch/stefan/7770410/working/building/REAL300020113736 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1084) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1084 `/scratch/stefan/7770410/working/3D/1084' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN2CCOC2=C1) `REAL300020113736.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113736 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN2CCOC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 13, 59, 89, 89, 89, 89, 89, 89, 89, 59, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13, 89, 89, 89, 89, 89] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 252 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113736 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN2CCOC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 102, 102, 102, 16, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 102, 201, 201, 201, 201, 201, 201, 201, 201, 201, 102, 102, 102, 102, 16, 6, 6, 4, 4, 102, 102, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 553 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113736 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN2CCOC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 56, 79, 102, 102, 102, 102, 13, 13, 1, 6, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 13, 56, 56, 79, 79, 1, 1, 14, 14, 14, 14, 14] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43]) total number of confs: 388 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113736 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN2CCOC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 14, 14, 14, 89, 89, 89, 165, 201, 201, 201, 201, 201, 89, 89, 14, 1, 1, 1, 1, 1, 1, 1, 1, 3, 14, 14, 14, 14, 89, 165, 165, 201, 201, 14, 14, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 39, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 716 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113736 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113736/1 /scratch/stefan/7770410/working/building/REAL300020113736 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1085) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1085 `/scratch/stefan/7770410/working/3D/1085' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN2CCOC2=C1) `REAL300020113736.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113736/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113736 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN2CCOC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 13, 59, 88, 88, 88, 88, 88, 88, 88, 59, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13, 88, 88, 88, 88, 88] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 250 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113736 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN2CCOC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 103, 103, 103, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 103, 201, 201, 201, 201, 201, 201, 201, 201, 201, 103, 103, 103, 103, 15, 6, 6, 4, 4, 103, 103, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 552 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113736 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN2CCOC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 58, 81, 104, 104, 104, 104, 13, 13, 1, 6, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 13, 58, 58, 81, 81, 1, 1, 14, 14, 14, 14, 14] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43]) total number of confs: 394 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113736 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN2CCOC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 14, 14, 14, 88, 88, 88, 166, 201, 201, 201, 201, 201, 88, 88, 14, 1, 1, 1, 1, 1, 1, 1, 1, 3, 14, 14, 14, 14, 88, 166, 166, 201, 201, 14, 14, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 39, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 720 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113736 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113736 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113736/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113736/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113736 Building REAL300020113737 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113737' /scratch/stefan/7770410/working/building/REAL300020113737 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113737 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113737/0 /scratch/stefan/7770410/working/building/REAL300020113737 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1086) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1086 `/scratch/stefan/7770410/working/3D/1086' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1CCOCC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113737.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113737 none O=C(CN1CCOCC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 30, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 11, 11, 11, 32, 48, 50, 50, 50, 50, 11, 11, 1, 30, 30, 33, 33, 33, 33, 33, 33, 6, 1, 1, 1, 1, 11, 32, 32, 48, 48, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 304 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113737 none O=C(CN1CCOCC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 107, 109, 109, 109, 109, 109, 109, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 107, 107, 109, 109, 109, 109, 109, 109, 35, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 415 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113737 none O=C(CN1CCOCC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 3, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 33, 33, 33, 109, 109, 109, 177, 201, 201, 201, 201, 201, 109, 109, 33, 3, 3, 1, 1, 1, 1, 1, 1, 12, 33, 33, 33, 33, 109, 177, 177, 201, 201, 33, 33] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 685 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113737 none O=C(CN1CCOCC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 200, 201, 201, 201, 201, 201, 201, 43, 43, 43, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 43, 200, 200, 201, 201, 201, 201, 201, 201, 102, 43, 43, 43, 43, 8, 4, 4, 2, 2, 43, 43] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 749 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113737 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113737/1 /scratch/stefan/7770410/working/building/REAL300020113737 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1087) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1087 `/scratch/stefan/7770410/working/3D/1087' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1CCOCC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113737.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113737/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113737 none O=C(CN1CCOCC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 30, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 11, 11, 11, 32, 48, 50, 50, 50, 50, 11, 11, 1, 30, 30, 33, 33, 33, 33, 33, 33, 6, 1, 1, 1, 1, 11, 32, 32, 48, 48, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 304 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113737 none O=C(CN1CCOCC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 107, 109, 109, 109, 109, 109, 109, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 107, 107, 109, 109, 109, 109, 109, 109, 36, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 414 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113737 none O=C(CN1CCOCC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 3, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 33, 33, 33, 109, 109, 109, 177, 201, 201, 201, 201, 201, 109, 109, 33, 3, 3, 1, 1, 1, 1, 1, 1, 12, 33, 33, 33, 33, 109, 177, 177, 201, 201, 33, 33] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 683 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113737 none O=C(CN1CCOCC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 200, 201, 201, 201, 201, 201, 201, 44, 44, 44, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 44, 200, 200, 201, 201, 201, 201, 201, 201, 102, 44, 44, 44, 44, 9, 4, 4, 2, 2, 44, 44] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 744 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113737 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113737 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113737/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113737/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113737 Building REAL300020113738 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113738' /scratch/stefan/7770410/working/building/REAL300020113738 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113738 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113738/0 /scratch/stefan/7770410/working/building/REAL300020113738 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1088) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1088 `/scratch/stefan/7770410/working/3D/1088' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=NNN=C2N=C1) `REAL300020113738.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113738 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=NNN=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 8, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 9, 9, 9, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 9, 32, 81, 81, 81, 81, 81, 81, 81, 81, 32, 9, 9, 9, 9, 1, 8, 8, 10, 10, 9, 9, 81, 81, 81] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 193 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113738 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=NNN=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 8, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 60, 60, 60, 13, 13, 13, 7, 4, 1, 1, 1, 1, 1, 1, 13, 13, 60, 104, 201, 201, 201, 201, 201, 201, 201, 201, 104, 60, 60, 60, 60, 13, 7, 7, 4, 4, 60, 60, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 457 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113738 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=NNN=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 8, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 32, 48, 58, 58, 58, 58, 9, 9, 1, 6, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 9, 32, 32, 48, 48, 1, 1, 16, 16, 16] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113738 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=NNN=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 8, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 16, 16, 16, 81, 81, 81, 156, 201, 201, 201, 201, 201, 81, 81, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 81, 156, 156, 201, 201, 16, 16, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 789 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113738 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113738/1 /scratch/stefan/7770410/working/building/REAL300020113738 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1089) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1089 `/scratch/stefan/7770410/working/3D/1089' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=NNN=C2N=C1) `REAL300020113738.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113738 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=NNN=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 8, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 9, 9, 9, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 9, 32, 81, 81, 81, 81, 81, 81, 81, 81, 32, 9, 9, 9, 9, 1, 8, 8, 10, 10, 9, 9, 81, 81, 81] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 193 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113738 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=NNN=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 8, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 60, 60, 60, 13, 13, 13, 7, 4, 1, 1, 1, 1, 1, 1, 13, 13, 60, 104, 201, 201, 201, 201, 201, 201, 201, 201, 104, 60, 60, 60, 60, 13, 7, 7, 4, 4, 60, 60, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 457 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113738 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=NNN=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 8, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 32, 48, 58, 58, 58, 58, 9, 9, 1, 6, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 9, 32, 32, 48, 48, 1, 1, 16, 16, 16] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113738 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=NNN=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 8, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 16, 16, 16, 81, 81, 81, 156, 201, 201, 201, 201, 201, 81, 81, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 81, 156, 156, 201, 201, 16, 16, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 789 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113738 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113738 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113738/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113738/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113738 Building REAL300020113739 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113739' /scratch/stefan/7770410/working/building/REAL300020113739 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113739 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113739/0 /scratch/stefan/7770410/working/building/REAL300020113739 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1090) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1090 `/scratch/stefan/7770410/working/3D/1090' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1) `REAL300020113739.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113739 none CCC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 7, 7, 7, 7, 7, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 43, 61, 75, 75, 75, 75, 12, 12, 1, 7, 21, 21, 21, 21, 21, 7, 7, 7, 6, 1, 1, 1, 1, 12, 43, 43, 61, 61, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 346 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113739 none CCC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 48, 48, 48, 48, 48, 46, 46, 46, 12, 12, 12, 1, 1, 1, 1, 1, 6, 8, 11, 11, 11, 11, 1, 1, 12, 48, 102, 102, 102, 102, 102, 48, 48, 48, 46, 12, 12, 12, 12, 1, 6, 6, 8, 8, 12, 12] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 447 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113739 none CCC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 48, 48, 48, 127, 155, 167, 167, 167, 167, 48, 48, 7, 1, 6, 6, 6, 6, 6, 1, 1, 1, 2, 7, 7, 7, 7, 48, 127, 127, 155, 155, 7, 7] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 625 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113739 none CCC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 167, 167, 167, 167, 167, 167, 167, 167, 75, 75, 75, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 75, 167, 201, 201, 201, 201, 201, 167, 167, 167, 167, 75, 75, 75, 75, 11, 6, 6, 4, 4, 75, 75] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 673 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113739 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113739/1 /scratch/stefan/7770410/working/building/REAL300020113739 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1091) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1091 `/scratch/stefan/7770410/working/3D/1091' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1) `REAL300020113739.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113739/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113739 none CCC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 7, 7, 7, 7, 7, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 43, 61, 74, 74, 74, 74, 12, 12, 1, 7, 20, 20, 20, 20, 20, 7, 7, 7, 6, 1, 1, 1, 1, 12, 43, 43, 61, 61, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 341 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113739 none CCC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 48, 48, 48, 48, 48, 46, 46, 46, 12, 12, 12, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 12, 48, 102, 102, 102, 102, 102, 48, 48, 48, 46, 12, 12, 12, 12, 1, 6, 6, 8, 8, 12, 12] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 445 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113739 none CCC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 48, 48, 48, 126, 154, 168, 168, 168, 168, 48, 48, 7, 1, 5, 5, 5, 5, 5, 1, 1, 1, 2, 7, 7, 7, 7, 48, 126, 126, 154, 154, 7, 7] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 623 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113739 none CCC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 167, 167, 167, 167, 167, 167, 167, 167, 75, 75, 75, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 75, 167, 201, 201, 201, 201, 201, 167, 167, 167, 167, 75, 75, 75, 75, 11, 6, 6, 4, 4, 75, 75] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 671 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113739 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113739 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113739/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113739/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113739 Building REAL300020113740 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113740' /scratch/stefan/7770410/working/building/REAL300020113740 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113740 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113740/0 /scratch/stefan/7770410/working/building/REAL300020113740 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1092) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1092 `/scratch/stefan/7770410/working/3D/1092' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=CC=NN2N=C1) `REAL300020113740.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113740 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=CC=NN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 38, 105, 105, 105, 105, 105, 105, 105, 105, 38, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 105, 105, 105, 105] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 225 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113740 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=CC=NN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 68, 68, 68, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 68, 133, 201, 201, 201, 201, 201, 201, 201, 201, 133, 68, 68, 68, 68, 12, 6, 6, 4, 4, 68, 68, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 477 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113740 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=CC=NN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 39, 55, 68, 68, 68, 68, 11, 11, 1, 6, 23, 23, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 11, 39, 39, 55, 55, 1, 1, 23, 23, 23, 23] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113740 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=CC=NN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 23, 23, 23, 105, 105, 105, 167, 201, 201, 201, 201, 201, 105, 105, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 23, 23, 23, 23, 105, 167, 167, 201, 201, 23, 23, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 703 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113740 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113740/1 /scratch/stefan/7770410/working/building/REAL300020113740 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1093) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1093 `/scratch/stefan/7770410/working/3D/1093' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=CC=NN2N=C1) `REAL300020113740.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113740 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=CC=NN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 38, 105, 105, 105, 105, 105, 105, 105, 105, 38, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 105, 105, 105, 105] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 225 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113740 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=CC=NN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 68, 68, 68, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 68, 133, 201, 201, 201, 201, 201, 201, 201, 201, 133, 68, 68, 68, 68, 12, 6, 6, 4, 4, 68, 68, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 477 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113740 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=CC=NN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 39, 55, 68, 68, 68, 68, 11, 11, 1, 6, 23, 23, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 11, 39, 39, 55, 55, 1, 1, 23, 23, 23, 23] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113740 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=CC=NN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 23, 23, 23, 105, 105, 105, 167, 201, 201, 201, 201, 201, 105, 105, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 23, 23, 23, 23, 105, 167, 167, 201, 201, 23, 23, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 703 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113740 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113740 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113740/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113740/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113740 Building REAL300020113741 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113741' /scratch/stefan/7770410/working/building/REAL300020113741 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113741 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113741/0 /scratch/stefan/7770410/working/building/REAL300020113741 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1094) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1094 `/scratch/stefan/7770410/working/3D/1094' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113741.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113741 none CC1=NN(C)C=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 37, 37, 18, 4, 4, 4, 1, 1, 1, 1, 1, 8, 8, 8, 21, 32, 32, 32, 32, 32, 8, 8, 1, 37, 37, 37, 37, 37, 37, 37, 18, 18, 4, 1, 1, 1, 1, 8, 21, 21, 32, 32, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 222 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113741 none CC1=NN(C)C=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 117, 117, 117, 117, 117, 70, 15, 15, 15, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 117, 117, 117, 117, 117, 117, 117, 70, 70, 15, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 361 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113741 none CC1=NN(C)C=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 23, 23, 23, 37, 37, 37, 117, 117, 117, 168, 201, 201, 201, 201, 201, 117, 117, 37, 2, 2, 2, 2, 2, 2, 1, 5, 5, 23, 37, 37, 37, 37, 117, 168, 168, 201, 201, 37, 37] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 705 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113741 none CC1=NN(C)C=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 145, 46, 46, 46, 34, 34, 34, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 34, 201, 201, 201, 201, 201, 201, 201, 145, 145, 46, 34, 34, 34, 34, 8, 4, 4, 2, 2, 34, 34] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 644 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113741 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113741/1 /scratch/stefan/7770410/working/building/REAL300020113741 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1095) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1095 `/scratch/stefan/7770410/working/3D/1095' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113741.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113741/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113741 none CC1=NN(C)C=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 37, 37, 18, 4, 4, 4, 1, 1, 1, 1, 1, 8, 8, 8, 21, 32, 32, 32, 32, 32, 8, 8, 1, 37, 37, 37, 37, 37, 37, 37, 18, 18, 4, 1, 1, 1, 1, 8, 21, 21, 32, 32, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 222 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113741 none CC1=NN(C)C=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 117, 117, 117, 117, 117, 70, 15, 15, 15, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 117, 117, 117, 117, 117, 117, 117, 70, 70, 15, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 361 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113741 none CC1=NN(C)C=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 23, 23, 23, 37, 37, 37, 117, 117, 117, 168, 201, 201, 201, 201, 201, 117, 117, 37, 2, 2, 2, 2, 2, 2, 1, 5, 5, 23, 37, 37, 37, 37, 117, 168, 168, 201, 201, 37, 37] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 705 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113741 none CC1=NN(C)C=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 145, 45, 45, 45, 33, 33, 33, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 33, 201, 201, 201, 201, 201, 201, 201, 145, 145, 45, 33, 33, 33, 33, 7, 4, 4, 2, 2, 33, 33] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 645 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113741 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113741 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113741/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113741/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113741 Building REAL300020113742 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113742' /scratch/stefan/7770410/working/building/REAL300020113742 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113742 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113742/0 /scratch/stefan/7770410/working/building/REAL300020113742 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1096) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1096 `/scratch/stefan/7770410/working/3D/1096' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C(F)F)=N1) `REAL300020113742.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113742 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 15, 15, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 22, 30, 32, 32, 32, 32, 5, 5, 1, 21, 21, 39, 39, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 5, 22, 22, 30, 30, 1, 1, 39] 101 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 240 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113742 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 15, 15, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 20, 20, 20, 5, 5, 5, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 5, 46, 46, 63, 63, 46, 46, 46, 46, 46, 20, 5, 5, 5, 5, 1, 8, 8, 10, 10, 5, 5, 63] 101 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 216 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113742 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 15, 15, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 8, 21, 21, 21, 46, 46, 46, 81, 99, 101, 101, 101, 101, 46, 46, 21, 1, 1, 8, 8, 1, 2, 2, 2, 1, 8, 21, 21, 21, 21, 46, 81, 81, 99, 99, 21, 21, 8] 101 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 27, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 398 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113742 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 15, 15, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 68, 68, 68, 35, 35, 35, 15, 15, 15, 7, 4, 1, 1, 1, 1, 1, 1, 15, 15, 35, 101, 101, 101, 101, 101, 101, 101, 101, 101, 68, 35, 35, 35, 35, 15, 7, 7, 4, 4, 35, 35, 101] 101 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 257 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113742 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113742/1 /scratch/stefan/7770410/working/building/REAL300020113742 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1097) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1097 `/scratch/stefan/7770410/working/3D/1097' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C(F)F)=N1) `REAL300020113742.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113742 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 15, 15, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 22, 30, 32, 32, 32, 32, 5, 5, 1, 21, 21, 39, 39, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 5, 22, 22, 30, 30, 1, 1, 39] 98 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 240 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113742 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 15, 15, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 20, 20, 20, 5, 5, 5, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 5, 46, 46, 61, 61, 46, 46, 46, 46, 46, 20, 5, 5, 5, 5, 1, 8, 8, 10, 10, 5, 5, 61] 98 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 204 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113742 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 15, 15, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 8, 21, 21, 21, 46, 46, 46, 80, 96, 98, 98, 98, 98, 46, 46, 21, 1, 1, 8, 8, 1, 2, 2, 2, 1, 8, 21, 21, 21, 21, 46, 80, 80, 96, 96, 21, 21, 8] 98 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 27, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 380 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113742 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 15, 15, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 65, 65, 65, 35, 35, 35, 15, 15, 15, 7, 4, 1, 1, 1, 1, 1, 1, 15, 15, 35, 98, 98, 98, 98, 98, 98, 98, 98, 98, 65, 35, 35, 35, 35, 15, 7, 7, 4, 4, 35, 35, 98] 98 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 251 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113742 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113742 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113742/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113742/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113742 Building REAL300020113743 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113743' /scratch/stefan/7770410/working/building/REAL300020113743 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113743 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113743/0 /scratch/stefan/7770410/working/building/REAL300020113743 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1098) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1098 `/scratch/stefan/7770410/working/3D/1098' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC1) `REAL300020113743.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113743 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 22, 64, 22, 22, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 64, 91, 91, 91, 91, 64, 64, 64, 64, 64, 64, 22, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 91, 91, 91, 91, 91, 91, 91, 91, 91] 201 rigid atoms, others: [38, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 361 number of broken/clashed sets: 167 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113743 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [98, 63, 98, 63, 63, 50, 50, 50, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 50, 98, 194, 194, 194, 194, 98, 98, 98, 98, 98, 98, 63, 50, 50, 50, 50, 12, 6, 6, 4, 4, 50, 50, 194, 194, 194, 194, 194, 194, 194, 194, 194] 194 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 658 number of broken/clashed sets: 147 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113743 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 16, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 25, 38, 38, 38, 38, 38, 8, 8, 1, 16, 24, 24, 24, 24, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 8, 25, 25, 38, 38, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 43, 44, 21, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 241 number of broken/clashed sets: 167 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113743 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 8, 8, 8, 24, 24, 24, 91, 91, 91, 155, 201, 201, 201, 201, 201, 91, 91, 24, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 8, 24, 24, 24, 24, 91, 155, 155, 201, 201, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 45, 46, 47, 48, 49, 50, 51, 52, 53, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 776 number of broken/clashed sets: 167 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113743 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113743/1 /scratch/stefan/7770410/working/building/REAL300020113743 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1099) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1099 `/scratch/stefan/7770410/working/3D/1099' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC1) `REAL300020113743.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113743/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113743 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 22, 64, 22, 22, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 64, 91, 91, 91, 91, 64, 64, 64, 64, 64, 64, 22, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 91, 91, 91, 91, 91, 91, 91, 91, 91] 201 rigid atoms, others: [38, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 361 number of broken/clashed sets: 167 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113743 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [98, 63, 98, 63, 63, 50, 50, 50, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 50, 98, 194, 194, 194, 194, 98, 98, 98, 98, 98, 98, 63, 50, 50, 50, 50, 12, 6, 6, 4, 4, 50, 50, 194, 194, 194, 194, 194, 194, 194, 194, 194] 194 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 658 number of broken/clashed sets: 147 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113743 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 16, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 25, 38, 38, 38, 38, 38, 8, 8, 1, 16, 24, 24, 24, 24, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 8, 25, 25, 38, 38, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 43, 44, 21, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 241 number of broken/clashed sets: 167 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113743 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 8, 8, 8, 24, 24, 24, 91, 91, 91, 155, 201, 201, 201, 201, 201, 91, 91, 24, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 8, 24, 24, 24, 24, 91, 155, 155, 201, 201, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 45, 46, 47, 48, 49, 50, 51, 52, 53, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 776 number of broken/clashed sets: 167 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113743 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113743 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113743/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113743/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113743 Building REAL300020113744 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113744' /scratch/stefan/7770410/working/building/REAL300020113744 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113744 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113744/0 /scratch/stefan/7770410/working/building/REAL300020113744 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1100) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1100 `/scratch/stefan/7770410/working/3D/1100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=NC=CN=C2N=C1) `REAL300020113744.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113744 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=NC=CN=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 8, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 11, 11, 11, 1, 1, 1, 1, 1, 5, 7, 10, 10, 10, 10, 1, 1, 11, 45, 109, 109, 109, 109, 109, 109, 109, 109, 109, 45, 11, 11, 11, 11, 1, 5, 5, 7, 7, 11, 11, 109, 109, 109, 109] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 240 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113744 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=NC=CN=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 8, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 66, 66, 66, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 66, 105, 201, 201, 201, 201, 201, 201, 201, 201, 201, 105, 66, 66, 66, 66, 10, 6, 6, 4, 4, 66, 66, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 456 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113744 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=NC=CN=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 8, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 34, 54, 66, 66, 66, 66, 11, 11, 1, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 11, 34, 34, 54, 54, 1, 1, 19, 19, 19, 19] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113744 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=NC=CN=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 8, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 19, 19, 19, 109, 109, 109, 176, 201, 201, 201, 201, 201, 109, 109, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 19, 19, 19, 19, 109, 176, 176, 201, 201, 19, 19, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 638 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113744 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113744/1 /scratch/stefan/7770410/working/building/REAL300020113744 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1101) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1101 `/scratch/stefan/7770410/working/3D/1101' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=NC=CN=C2N=C1) `REAL300020113744.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113744/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113744 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=NC=CN=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 8, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 11, 11, 11, 1, 1, 1, 1, 1, 5, 7, 10, 10, 10, 10, 1, 1, 11, 45, 109, 109, 109, 109, 109, 109, 109, 109, 109, 45, 11, 11, 11, 11, 1, 5, 5, 7, 7, 11, 11, 109, 109, 109, 109] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 240 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113744 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=NC=CN=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 8, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 66, 66, 66, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 66, 103, 201, 201, 201, 201, 201, 201, 201, 201, 201, 103, 66, 66, 66, 66, 10, 6, 6, 4, 4, 66, 66, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 453 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113744 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=NC=CN=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 8, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 34, 54, 66, 66, 66, 66, 11, 11, 1, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 11, 34, 34, 54, 54, 1, 1, 19, 19, 19, 19] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113744 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=NC=CN=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 8, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 19, 19, 19, 109, 109, 109, 176, 201, 201, 201, 201, 201, 109, 109, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 19, 19, 19, 19, 109, 176, 176, 201, 201, 19, 19, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 638 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113744 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113744 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113744/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113744/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113744 Building REAL300020113745 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113745' /scratch/stefan/7770410/working/building/REAL300020113745 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113745 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113745/0 /scratch/stefan/7770410/working/building/REAL300020113745 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1102) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1102 `/scratch/stefan/7770410/working/3D/1102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCCCC1) `REAL300020113745.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113745 none CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 61, 83, 87, 87, 87, 87, 13, 13, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 13, 61, 61, 83, 83, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 190 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 41, 40, 20, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 346 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113745 none CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 56, 13, 13, 13, 1, 1, 1, 1, 1, 8, 12, 16, 16, 16, 16, 1, 1, 13, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 13, 13, 13, 13, 1, 8, 8, 12, 12, 13, 13, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56] 190 rigid atoms, others: [35, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 193 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113745 none CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 2, 2, 2, 6, 6, 6, 56, 56, 56, 150, 190, 190, 190, 190, 190, 56, 56, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 6, 6, 6, 6, 56, 150, 150, 190, 190, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 190 rigid atoms, others: [0, 1, 2, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 21, 22, 23, 24, 25, 26, 53] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 754 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113745 none CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 189, 189, 86, 86, 86, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 86, 189, 189, 189, 189, 189, 189, 189, 189, 189, 189, 86, 86, 86, 86, 17, 6, 6, 4, 4, 86, 86, 189, 189, 189, 189, 189, 189, 189, 189, 189, 189, 189, 189] 189 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 511 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113745 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113745/1 /scratch/stefan/7770410/working/building/REAL300020113745 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1103) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1103 `/scratch/stefan/7770410/working/3D/1103' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCCCC1) `REAL300020113745.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113745 none CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 62, 84, 89, 89, 89, 89, 13, 13, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 13, 62, 62, 84, 84, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 192 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 41, 40, 20, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 351 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113745 none CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 56, 13, 13, 13, 1, 1, 1, 1, 1, 8, 12, 16, 16, 16, 16, 1, 1, 13, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 13, 13, 13, 13, 1, 8, 8, 12, 12, 13, 13, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56] 192 rigid atoms, others: [35, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 193 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113745 none CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 2, 2, 2, 6, 6, 6, 56, 56, 56, 151, 192, 192, 192, 192, 192, 56, 56, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 6, 6, 6, 6, 56, 151, 151, 192, 192, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 192 rigid atoms, others: [0, 1, 2, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 21, 22, 23, 24, 25, 26, 53] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 760 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113745 none CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [190, 190, 190, 190, 88, 88, 88, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 88, 190, 190, 190, 190, 190, 190, 190, 190, 190, 190, 88, 88, 88, 88, 18, 6, 6, 4, 4, 88, 88, 190, 190, 190, 190, 190, 190, 190, 190, 190, 190, 190, 190] 190 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 514 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113745 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113745 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113745/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113745/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113745 Building REAL300020113746 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113746' /scratch/stefan/7770410/working/building/REAL300020113746 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113746 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113746/0 /scratch/stefan/7770410/working/building/REAL300020113746 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1104) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1104 `/scratch/stefan/7770410/working/3D/1104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NOC(CC)=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113746.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113746 none CCC1=NOC(CC)=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 34, 34, 34, 34, 34, 34, 68, 17, 3, 3, 3, 1, 1, 1, 1, 1, 7, 7, 7, 18, 28, 28, 28, 28, 28, 7, 7, 1, 52, 52, 52, 52, 52, 68, 68, 68, 68, 68, 17, 17, 3, 1, 1, 1, 1, 7, 18, 18, 28, 28, 1, 1] 201 rigid atoms, others: [45, 44, 42, 43, 12, 13, 14, 15, 16, 51, 52, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50]) total number of confs: 485 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113746 none CCC1=NOC(CC)=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 80, 80, 80, 80, 80, 80, 129, 45, 13, 13, 13, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 112, 112, 112, 112, 112, 129, 129, 129, 129, 129, 45, 45, 13, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [46, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 721 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113746 none CCC1=NOC(CC)=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 5, 1, 1, 6, 20, 20, 20, 34, 34, 34, 80, 80, 80, 114, 144, 144, 144, 144, 144, 80, 80, 34, 5, 5, 5, 4, 4, 5, 5, 6, 6, 6, 6, 6, 20, 34, 34, 34, 34, 80, 114, 114, 144, 144, 34, 34] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 8, 9] set([0, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 580 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113746 none CCC1=NOC(CC)=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [183, 137, 137, 137, 137, 137, 137, 174, 80, 24, 24, 24, 24, 24, 24, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 24, 183, 183, 183, 183, 183, 174, 174, 174, 174, 174, 80, 80, 24, 24, 24, 24, 24, 7, 4, 4, 2, 2, 24, 24] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 894 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113746 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113746/1 /scratch/stefan/7770410/working/building/REAL300020113746 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1105) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1105 `/scratch/stefan/7770410/working/3D/1105' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NOC(CC)=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113746.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113746/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113746 none CCC1=NOC(CC)=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 34, 34, 34, 34, 34, 34, 67, 17, 3, 3, 3, 1, 1, 1, 1, 1, 7, 7, 7, 18, 28, 28, 28, 28, 28, 7, 7, 1, 51, 51, 51, 51, 51, 67, 67, 67, 67, 67, 17, 17, 3, 1, 1, 1, 1, 7, 18, 18, 28, 28, 1, 1] 201 rigid atoms, others: [45, 44, 42, 43, 12, 13, 14, 15, 16, 51, 52, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50]) total number of confs: 473 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113746 none CCC1=NOC(CC)=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 84, 84, 84, 84, 84, 84, 129, 46, 13, 13, 13, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 115, 115, 115, 115, 115, 129, 129, 129, 129, 129, 46, 46, 13, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [46, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 706 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113746 none CCC1=NOC(CC)=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 5, 1, 1, 6, 20, 20, 20, 34, 34, 34, 84, 84, 84, 116, 146, 146, 146, 146, 146, 84, 84, 34, 5, 5, 5, 4, 4, 5, 5, 6, 6, 6, 6, 6, 20, 34, 34, 34, 34, 84, 116, 116, 146, 146, 34, 34] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 8, 9] set([0, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 575 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113746 none CCC1=NOC(CC)=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [184, 138, 138, 138, 138, 138, 138, 174, 82, 24, 24, 24, 24, 24, 24, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 24, 184, 184, 184, 184, 184, 174, 174, 174, 174, 174, 82, 82, 24, 24, 24, 24, 24, 7, 4, 4, 2, 2, 24, 24] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 892 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113746 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113746 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113746/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113746/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113746 Building REAL300020113747 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113747' /scratch/stefan/7770410/working/building/REAL300020113747 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113747 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113747/0 /scratch/stefan/7770410/working/building/REAL300020113747 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1106) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1106 `/scratch/stefan/7770410/working/3D/1106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=CN=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113747.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113747 none COC1=CC(C)=CN=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 41, 57, 63, 63, 63, 63, 13, 13, 1, 29, 29, 29, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 13, 41, 41, 57, 57, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 279 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113747 none COC1=CC(C)=CN=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 96, 96, 96, 96, 96, 96, 96, 49, 49, 49, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 118, 118, 118, 96, 96, 96, 96, 96, 49, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 275 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113747 none COC1=CC(C)=CN=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 22, 22, 22, 96, 96, 96, 170, 197, 201, 201, 201, 201, 96, 96, 22, 4, 4, 4, 1, 2, 2, 2, 1, 7, 22, 22, 22, 22, 96, 170, 170, 197, 197, 22, 22] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 31] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 674 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113747 none COC1=CC(C)=CN=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 174, 174, 174, 67, 67, 67, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 67, 201, 201, 201, 201, 201, 201, 201, 201, 174, 67, 67, 67, 67, 10, 6, 6, 4, 4, 67, 67] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 523 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113747 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113747/1 /scratch/stefan/7770410/working/building/REAL300020113747 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1107) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1107 `/scratch/stefan/7770410/working/3D/1107' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=CN=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113747.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113747 none COC1=CC(C)=CN=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 41, 57, 63, 63, 63, 63, 13, 13, 1, 29, 29, 29, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 13, 41, 41, 57, 57, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 279 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113747 none COC1=CC(C)=CN=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 95, 95, 95, 95, 95, 95, 95, 49, 49, 49, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 118, 118, 118, 95, 95, 95, 95, 95, 49, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 275 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113747 none COC1=CC(C)=CN=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 22, 22, 22, 95, 95, 95, 171, 197, 201, 201, 201, 201, 95, 95, 22, 4, 4, 4, 1, 2, 2, 2, 1, 7, 22, 22, 22, 22, 95, 171, 171, 197, 197, 22, 22] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 31] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 679 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113747 none COC1=CC(C)=CN=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 174, 174, 174, 68, 68, 68, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 68, 201, 201, 201, 201, 201, 201, 201, 201, 174, 68, 68, 68, 68, 12, 6, 6, 4, 4, 68, 68] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 522 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113747 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113747 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113747/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113747/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113747 Building REAL300020113748 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113748' /scratch/stefan/7770410/working/building/REAL300020113748 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113748 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113748/0 /scratch/stefan/7770410/working/building/REAL300020113748 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1108) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1108 `/scratch/stefan/7770410/working/3D/1108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC2=NC=CN12) `REAL300020113748.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113748 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC2=NC=CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 34, 50, 54, 54, 54, 54, 11, 11, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 34, 34, 50, 50, 1, 1, 22, 22] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 42, 21, 41] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44]) total number of confs: 241 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113748 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC2=NC=CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 33, 33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 98, 98, 98, 98, 98, 98, 98, 98, 98, 33, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 98, 98] 201 rigid atoms, others: [36, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 205 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113748 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC2=NC=CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 22, 22, 22, 98, 98, 98, 153, 201, 201, 201, 201, 201, 98, 98, 22, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 22, 22, 22, 22, 98, 153, 153, 201, 201, 22, 22, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 43, 44, 22, 23, 24, 25, 26, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 740 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113748 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SC2=NC=CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 117, 117, 117, 57, 57, 57, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 57, 201, 201, 201, 201, 201, 201, 201, 201, 201, 117, 57, 57, 57, 57, 12, 6, 6, 4, 4, 57, 57, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 464 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113748 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113748/1 /scratch/stefan/7770410/working/building/REAL300020113748 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1109) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1109 `/scratch/stefan/7770410/working/3D/1109' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC2=NC=CN12) `REAL300020113748.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113748 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC2=NC=CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 34, 50, 54, 54, 54, 54, 11, 11, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 34, 34, 50, 50, 1, 1, 22, 22] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 42, 21, 41] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44]) total number of confs: 241 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113748 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC2=NC=CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 33, 33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 98, 98, 98, 98, 98, 98, 98, 98, 98, 33, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 98, 98] 201 rigid atoms, others: [36, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 205 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113748 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC2=NC=CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 22, 22, 22, 98, 98, 98, 153, 201, 201, 201, 201, 201, 98, 98, 22, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 22, 22, 22, 22, 98, 153, 153, 201, 201, 22, 22, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 43, 44, 22, 23, 24, 25, 26, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 740 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113748 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SC2=NC=CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 1, 8, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 115, 115, 115, 56, 56, 56, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 56, 201, 201, 201, 201, 201, 201, 201, 201, 201, 115, 56, 56, 56, 56, 13, 6, 6, 4, 4, 56, 56, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 460 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113748 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113748 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113748/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113748/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113748 Building REAL300020113749 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113749' /scratch/stefan/7770410/working/building/REAL300020113749 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113749 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113749/0 /scratch/stefan/7770410/working/building/REAL300020113749 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1110) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1110 `/scratch/stefan/7770410/working/3D/1110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=C(C=N1)OCCO2) `REAL300020113749.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113749 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=C(C=N1)OCCO2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 12, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 20, 20, 20, 20, 1, 1, 13, 52, 94, 94, 94, 94, 94, 94, 94, 94, 94, 52, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 94, 94, 94, 94, 94, 94] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 263 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113749 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=C(C=N1)OCCO2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 12, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [191, 191, 108, 108, 108, 24, 24, 24, 6, 4, 1, 1, 1, 1, 1, 1, 24, 24, 108, 191, 201, 201, 201, 201, 201, 201, 201, 201, 201, 191, 108, 108, 108, 108, 24, 6, 6, 4, 4, 108, 108, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 535 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113749 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=C(C=N1)OCCO2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 12, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 67, 89, 107, 107, 107, 107, 13, 13, 1, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 13, 67, 67, 89, 89, 1, 1, 19, 19, 19, 19, 19, 19] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 407 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113749 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=C(C=N1)OCCO2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 12, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 19, 19, 19, 94, 94, 94, 165, 201, 201, 201, 201, 201, 94, 94, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 19, 19, 19, 19, 94, 165, 165, 201, 201, 19, 19, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 696 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113749 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113749/1 /scratch/stefan/7770410/working/building/REAL300020113749 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1111) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1111 `/scratch/stefan/7770410/working/3D/1111' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=C(C=N1)OCCO2) `REAL300020113749.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113749/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113749 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=C(C=N1)OCCO2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 12, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 20, 20, 20, 20, 1, 1, 13, 53, 96, 96, 96, 96, 96, 96, 96, 96, 96, 53, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 96, 96, 96, 96, 96, 96] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 267 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113749 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=C(C=N1)OCCO2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 12, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [191, 191, 107, 107, 107, 24, 24, 24, 6, 4, 1, 1, 1, 1, 1, 1, 24, 24, 107, 191, 201, 201, 201, 201, 201, 201, 201, 201, 201, 191, 107, 107, 107, 107, 24, 6, 6, 4, 4, 107, 107, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 535 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113749 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=C(C=N1)OCCO2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 12, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 67, 89, 107, 107, 107, 107, 13, 13, 1, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 13, 67, 67, 89, 89, 1, 1, 19, 19, 19, 19, 19, 19] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 407 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113749 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=C(C=N1)OCCO2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 12, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 19, 19, 19, 96, 96, 96, 165, 201, 201, 201, 201, 201, 96, 96, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 19, 19, 19, 19, 96, 165, 165, 201, 201, 19, 19, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 686 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113749 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113749 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113749/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113749/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113749 Building REAL300020113750 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113750' /scratch/stefan/7770410/working/building/REAL300020113750 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113750 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113750/0 /scratch/stefan/7770410/working/building/REAL300020113750 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1112) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1112 `/scratch/stefan/7770410/working/3D/1112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(F)C=N1) `REAL300020113750.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113750 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(F)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 15, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 13, 13, 13, 1, 1, 1, 1, 1, 7, 9, 9, 9, 9, 9, 1, 1, 13, 57, 95, 95, 95, 95, 95, 95, 57, 13, 13, 13, 13, 1, 7, 7, 9, 9, 13, 13, 95, 95, 95] 127 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 240 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113750 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(F)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 15, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 44, 44, 44, 10, 10, 10, 4, 2, 1, 1, 1, 1, 1, 1, 10, 10, 44, 100, 127, 127, 127, 127, 127, 127, 100, 44, 44, 44, 44, 10, 4, 4, 2, 2, 44, 44, 127, 127, 127] 127 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 336 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113750 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(F)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 15, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 31, 43, 43, 43, 43, 43, 13, 13, 1, 6, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 13, 31, 31, 43, 43, 1, 1, 23, 23, 23] 127 rigid atoms, others: [2, 3, 4, 5, 6, 18, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113750 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(F)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 15, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 23, 23, 23, 95, 95, 95, 121, 127, 127, 127, 127, 127, 95, 95, 23, 1, 1, 1, 1, 1, 1, 1, 9, 23, 23, 23, 23, 95, 121, 121, 127, 127, 23, 23, 1, 1, 1] 127 rigid atoms, others: [1, 38, 39, 40, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 318 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113750 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113750/1 /scratch/stefan/7770410/working/building/REAL300020113750 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1113) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1113 `/scratch/stefan/7770410/working/3D/1113' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(F)C=N1) `REAL300020113750.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113750 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(F)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 15, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 13, 13, 13, 1, 1, 1, 1, 1, 7, 9, 9, 9, 9, 9, 1, 1, 13, 57, 95, 95, 95, 95, 95, 95, 57, 13, 13, 13, 13, 1, 7, 7, 9, 9, 13, 13, 95, 95, 95] 130 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 240 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113750 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(F)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 15, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 45, 45, 45, 10, 10, 10, 4, 2, 1, 1, 1, 1, 1, 1, 10, 10, 45, 103, 130, 130, 130, 130, 130, 130, 103, 45, 45, 45, 45, 10, 4, 4, 2, 2, 45, 45, 130, 130, 130] 130 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 348 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113750 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(F)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 15, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 32, 44, 44, 44, 44, 44, 13, 13, 1, 6, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 13, 32, 32, 44, 44, 1, 1, 23, 23, 23] 130 rigid atoms, others: [2, 3, 4, 5, 6, 18, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113750 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(F)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 15, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 23, 23, 23, 95, 95, 95, 123, 130, 130, 130, 130, 130, 95, 95, 23, 1, 1, 1, 1, 1, 1, 1, 9, 23, 23, 23, 23, 95, 123, 123, 130, 130, 23, 23, 1, 1, 1] 130 rigid atoms, others: [1, 38, 39, 40, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 330 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113750 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113750 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113750/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113750/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113750 Building REAL300020113751 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113751' /scratch/stefan/7770410/working/building/REAL300020113751 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113751 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113751/0 /scratch/stefan/7770410/working/building/REAL300020113751 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1114) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1114 `/scratch/stefan/7770410/working/3D/1114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(CC2=CC=CC=C2)CC1) `REAL300020113751.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113751 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(CC2=CC=CC=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 10, 38, 69, 89, 89, 89, 89, 89, 89, 69, 69, 38, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 89, 89, 89, 89, 89, 89, 89, 69, 69, 69, 69] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 371 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113751 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(CC2=CC=CC=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 22, 22, 22, 89, 89, 89, 167, 201, 201, 201, 201, 201, 89, 89, 22, 2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 22, 22, 22, 22, 89, 167, 167, 201, 201, 22, 22, 2, 2, 1, 1, 1, 1, 1, 6, 6, 6, 6] 201 rigid atoms, others: [43, 44, 45, 46, 47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50, 51]) total number of confs: 734 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113751 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(CC2=CC=CC=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 44, 44, 44, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 44, 131, 200, 201, 201, 201, 201, 201, 201, 200, 200, 131, 44, 44, 44, 44, 10, 6, 6, 4, 4, 44, 44, 201, 201, 201, 201, 201, 201, 201, 200, 200, 200, 200] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 633 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113751 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(CC2=CC=CC=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 32, 43, 44, 44, 44, 44, 10, 10, 1, 6, 11, 22, 22, 22, 22, 22, 22, 11, 11, 6, 1, 1, 1, 1, 10, 32, 32, 43, 43, 1, 1, 22, 22, 22, 22, 22, 22, 22, 11, 11, 11, 11] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113751 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(CC2=CC=CC=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 11, 11, 11, 69, 69, 69, 150, 200, 200, 200, 200, 200, 69, 69, 11, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 3, 11, 11, 11, 11, 69, 150, 150, 200, 200, 11, 11, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [1, 51, 48, 49, 50, 19, 20, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 806 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113751 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113751/1 /scratch/stefan/7770410/working/building/REAL300020113751 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1115) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1115 `/scratch/stefan/7770410/working/3D/1115' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(CC2=CC=CC=C2)CC1) `REAL300020113751.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113751/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113751 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(CC2=CC=CC=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 10, 38, 69, 88, 88, 88, 88, 88, 88, 69, 69, 38, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 88, 88, 88, 88, 88, 88, 88, 69, 69, 69, 69] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 365 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113751 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(CC2=CC=CC=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 22, 22, 22, 88, 88, 88, 167, 201, 201, 201, 201, 201, 88, 88, 22, 2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 22, 22, 22, 22, 88, 167, 167, 201, 201, 22, 22, 2, 2, 1, 1, 1, 1, 1, 6, 6, 6, 6] 201 rigid atoms, others: [43, 44, 45, 46, 47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50, 51]) total number of confs: 739 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113751 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(CC2=CC=CC=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 44, 44, 44, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 44, 131, 200, 201, 201, 201, 201, 201, 201, 200, 200, 131, 44, 44, 44, 44, 10, 6, 6, 4, 4, 44, 44, 201, 201, 201, 201, 201, 201, 201, 200, 200, 200, 200] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 633 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113751 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(CC2=CC=CC=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 32, 43, 44, 44, 44, 44, 10, 10, 1, 6, 11, 22, 22, 22, 22, 22, 22, 11, 11, 6, 1, 1, 1, 1, 10, 32, 32, 43, 43, 1, 1, 22, 22, 22, 22, 22, 22, 22, 11, 11, 11, 11] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113751 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(CC2=CC=CC=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 11, 11, 11, 69, 69, 69, 150, 200, 200, 200, 200, 200, 69, 69, 11, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 3, 11, 11, 11, 11, 69, 150, 150, 200, 200, 11, 11, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [1, 51, 48, 49, 50, 19, 20, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 806 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113751 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113751 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113751/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113751/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113751 Building REAL300020113752 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113752' /scratch/stefan/7770410/working/building/REAL300020113752 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113752 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113752/0 /scratch/stefan/7770410/working/building/REAL300020113752 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1116) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1116 `/scratch/stefan/7770410/working/3D/1116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1NC(=O)N2) `REAL300020113752.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113752 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1NC(=O)N2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 8, 10, 11, 11, 11, 11, 1, 1, 6, 17, 38, 38, 38, 38, 38, 38, 38, 38, 38, 17, 6, 6, 6, 6, 1, 8, 8, 10, 10, 6, 6, 38, 38, 38, 38, 38] 74 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 111 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113752 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1NC(=O)N2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 32, 32, 32, 13, 13, 13, 6, 3, 1, 1, 1, 1, 1, 1, 13, 13, 32, 44, 74, 74, 74, 74, 74, 74, 74, 74, 74, 44, 32, 32, 32, 32, 13, 6, 6, 3, 3, 32, 32, 74, 74, 74, 74, 74] 74 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 177 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113752 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1NC(=O)N2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 22, 30, 31, 31, 31, 31, 6, 6, 1, 6, 22, 23, 23, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 6, 22, 22, 30, 30, 1, 1, 23, 23, 23, 23, 23] 74 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113752 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1NC(=O)N2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 23, 23, 23, 38, 38, 38, 66, 74, 74, 74, 74, 74, 38, 38, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 23, 23, 23, 23, 38, 66, 66, 74, 74, 23, 23, 1, 1, 1, 1, 1] 74 rigid atoms, others: [1, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 264 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113752 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113752/1 /scratch/stefan/7770410/working/building/REAL300020113752 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1117) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1117 `/scratch/stefan/7770410/working/3D/1117' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1NC(=O)N2) `REAL300020113752.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113752/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113752 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1NC(=O)N2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 8, 10, 11, 11, 11, 11, 1, 1, 6, 17, 38, 38, 38, 38, 38, 38, 38, 38, 38, 17, 6, 6, 6, 6, 1, 8, 8, 10, 10, 6, 6, 38, 38, 38, 38, 38] 74 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 111 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113752 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1NC(=O)N2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 32, 32, 32, 13, 13, 13, 6, 3, 1, 1, 1, 1, 1, 1, 13, 13, 32, 44, 74, 74, 74, 74, 74, 74, 74, 74, 74, 44, 32, 32, 32, 32, 13, 6, 6, 3, 3, 32, 32, 74, 74, 74, 74, 74] 74 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 177 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113752 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1NC(=O)N2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 22, 30, 31, 31, 31, 31, 6, 6, 1, 6, 22, 23, 23, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 6, 22, 22, 30, 30, 1, 1, 23, 23, 23, 23, 23] 74 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113752 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1NC(=O)N2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 23, 23, 23, 38, 38, 38, 66, 74, 74, 74, 74, 74, 38, 38, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 23, 23, 23, 23, 38, 66, 66, 74, 74, 23, 23, 1, 1, 1, 1, 1] 74 rigid atoms, others: [1, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 264 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113752 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113752 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113752/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113752/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113752 Building REAL300020113753 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113753' /scratch/stefan/7770410/working/building/REAL300020113753 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113753 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113753/0 /scratch/stefan/7770410/working/building/REAL300020113753 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1118) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1118 `/scratch/stefan/7770410/working/3D/1118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2CCCCN2C=C1) `REAL300020113753.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113753 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2CCCCN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 5, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 52, 117, 117, 117, 117, 117, 117, 117, 117, 52, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 270 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113753 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2CCCCN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 5, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [166, 166, 65, 65, 65, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 65, 166, 201, 201, 201, 201, 201, 201, 201, 201, 166, 65, 65, 65, 65, 11, 6, 6, 4, 4, 65, 65, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 516 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113753 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2CCCCN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 5, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 41, 59, 64, 64, 64, 64, 13, 13, 1, 6, 24, 24, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 13, 41, 41, 59, 59, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 281 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113753 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2CCCCN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 5, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 24, 24, 24, 117, 117, 117, 172, 201, 201, 201, 201, 201, 117, 117, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 24, 24, 24, 24, 117, 172, 172, 201, 201, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 628 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113753 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113753/1 /scratch/stefan/7770410/working/building/REAL300020113753 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1119) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1119 `/scratch/stefan/7770410/working/3D/1119' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2CCCCN2C=C1) `REAL300020113753.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113753/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113753 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2CCCCN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 5, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 51, 117, 117, 117, 117, 117, 117, 117, 117, 51, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 269 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113753 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2CCCCN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 5, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 65, 65, 65, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 65, 165, 201, 201, 201, 201, 201, 201, 201, 201, 165, 65, 65, 65, 65, 11, 6, 6, 4, 4, 65, 65, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 516 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113753 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2CCCCN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 5, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 40, 58, 63, 63, 63, 63, 13, 13, 1, 6, 25, 25, 25, 25, 25, 25, 25, 25, 6, 1, 1, 1, 1, 13, 40, 40, 58, 58, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113753 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2CCCCN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 5, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 25, 25, 25, 117, 117, 117, 172, 201, 201, 201, 201, 201, 117, 117, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 25, 25, 25, 25, 117, 172, 172, 201, 201, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 629 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113753 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113753 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113753/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113753/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113753 Building REAL300020113754 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113754' /scratch/stefan/7770410/working/building/REAL300020113754 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113754 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113754/0 /scratch/stefan/7770410/working/building/REAL300020113754 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1120) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1120 `/scratch/stefan/7770410/working/3D/1120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COCC1CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113754.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113754 none O=C(COCC1CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 12, 21, 25, 42, 42, 42, 42, 1, 1, 1, 1, 1, 7, 7, 7, 18, 30, 30, 30, 30, 30, 7, 7, 1, 12, 12, 25, 25, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 1, 1, 1, 1, 7, 18, 18, 30, 30, 1, 1] 201 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 44, 50, 51, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 258 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113754 none O=C(COCC1CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 44, 55, 59, 112, 112, 112, 112, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 44, 44, 59, 59, 112, 112, 112, 112, 112, 112, 112, 112, 112, 19, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [45, 14, 13, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 391 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113754 none O=C(COCC1CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 20, 8, 5, 1, 1, 1, 1, 1, 1, 29, 29, 42, 42, 42, 112, 112, 112, 171, 201, 201, 201, 201, 201, 112, 112, 42, 20, 20, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 42, 42, 42, 42, 112, 171, 171, 201, 201, 42, 42] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 39, 36, 38, 37, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 740 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113754 none O=C(COCC1CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 96, 111, 114, 201, 201, 201, 201, 31, 31, 31, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 31, 96, 96, 114, 114, 201, 201, 201, 201, 201, 201, 201, 201, 201, 46, 31, 31, 31, 31, 8, 4, 4, 2, 2, 31, 31] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 696 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113754 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113754/1 /scratch/stefan/7770410/working/building/REAL300020113754 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1121) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1121 `/scratch/stefan/7770410/working/3D/1121' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COCC1CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113754.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113754 none O=C(COCC1CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 12, 21, 25, 42, 42, 42, 42, 1, 1, 1, 1, 1, 7, 7, 7, 18, 30, 30, 30, 30, 30, 7, 7, 1, 12, 12, 25, 25, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 1, 1, 1, 1, 7, 18, 18, 30, 30, 1, 1] 201 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 44, 50, 51, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 258 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113754 none O=C(COCC1CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 44, 55, 59, 112, 112, 112, 112, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 44, 44, 59, 59, 112, 112, 112, 112, 112, 112, 112, 112, 112, 19, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [45, 14, 13, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 391 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113754 none O=C(COCC1CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 20, 8, 5, 1, 1, 1, 1, 1, 1, 29, 29, 42, 42, 42, 112, 112, 112, 171, 201, 201, 201, 201, 201, 112, 112, 42, 20, 20, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 42, 42, 42, 42, 112, 171, 171, 201, 201, 42, 42] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 39, 36, 38, 37, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 740 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113754 none O=C(COCC1CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 97, 112, 115, 201, 201, 201, 201, 32, 32, 32, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 32, 97, 97, 115, 115, 201, 201, 201, 201, 201, 201, 201, 201, 201, 47, 32, 32, 32, 32, 8, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 696 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113754 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113754 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113754/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113754/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113754 Building REAL300020113755 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113755' /scratch/stefan/7770410/working/building/REAL300020113755 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113755 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113755/0 /scratch/stefan/7770410/working/building/REAL300020113755 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1122) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1122 `/scratch/stefan/7770410/working/3D/1122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1) `REAL300020113755.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113755 none CCC1=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 13, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 28, 37, 37, 37, 37, 37, 13, 13, 1, 13, 13, 31, 31, 31, 31, 31, 6, 1, 1, 1, 1, 13, 28, 28, 37, 37, 1, 1, 13] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 254 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113755 none CCC1=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 69, 69, 69, 69, 48, 48, 48, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 13, 69, 69, 133, 133, 133, 133, 133, 48, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 69] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 566 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113755 none CCC1=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 69, 69, 69, 95, 107, 107, 107, 107, 107, 69, 69, 13, 1, 1, 4, 4, 4, 4, 4, 5, 13, 13, 13, 13, 69, 95, 95, 107, 107, 13, 13, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 44, 25, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 325 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113755 none CCC1=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 109, 109, 109, 109, 86, 86, 86, 40, 40, 40, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 40, 109, 109, 201, 201, 201, 201, 201, 86, 40, 40, 40, 40, 8, 4, 4, 2, 2, 40, 40, 109] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 845 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113755 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113755/1 /scratch/stefan/7770410/working/building/REAL300020113755 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1123) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1123 `/scratch/stefan/7770410/working/3D/1123' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1) `REAL300020113755.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113755/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113755 none CCC1=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 13, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 28, 37, 37, 37, 37, 37, 13, 13, 1, 13, 13, 31, 31, 31, 31, 31, 6, 1, 1, 1, 1, 13, 28, 28, 37, 37, 1, 1, 13] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 254 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113755 none CCC1=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 69, 69, 69, 69, 48, 48, 48, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 13, 69, 69, 133, 133, 133, 133, 133, 48, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 69] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 566 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113755 none CCC1=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 69, 69, 69, 96, 108, 108, 108, 108, 108, 69, 69, 13, 1, 1, 4, 4, 4, 4, 4, 5, 13, 13, 13, 13, 69, 96, 96, 108, 108, 13, 13, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 44, 25, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 331 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113755 none CCC1=C(Cl)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 108, 108, 108, 108, 85, 85, 85, 39, 39, 39, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 39, 108, 108, 201, 201, 201, 201, 201, 85, 39, 39, 39, 39, 8, 4, 4, 2, 2, 39, 39, 108] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 850 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113755 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113755 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113755/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113755/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113755 Building REAL300020113756 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113756' /scratch/stefan/7770410/working/building/REAL300020113756 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113756 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113756/0 /scratch/stefan/7770410/working/building/REAL300020113756 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1124) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1124 `/scratch/stefan/7770410/working/3D/1124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC=CC2=CC=CN=C21) `REAL300020113756.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113756 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC=CC2=CC=CN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 13, 54, 107, 107, 107, 107, 107, 107, 107, 107, 107, 54, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13, 107, 107, 107, 107, 107] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 261 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113756 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC=CC2=CC=CN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 163, 75, 75, 75, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 75, 163, 201, 201, 201, 201, 201, 201, 201, 201, 201, 163, 75, 75, 75, 75, 13, 6, 6, 4, 4, 75, 75, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 507 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113756 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC=CC2=CC=CN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 47, 66, 74, 74, 74, 74, 13, 13, 1, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 13, 47, 47, 66, 66, 1, 1, 24, 24, 24, 24, 24] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 311 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113756 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC=CC2=CC=CN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 24, 24, 24, 107, 107, 107, 178, 201, 201, 201, 201, 201, 107, 107, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 24, 24, 24, 24, 107, 178, 178, 201, 201, 24, 24, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 650 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113756 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113756/1 /scratch/stefan/7770410/working/building/REAL300020113756 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1125) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1125 `/scratch/stefan/7770410/working/3D/1125' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC=CC2=CC=CN=C21) `REAL300020113756.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113756 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC=CC2=CC=CN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 13, 54, 107, 107, 107, 107, 107, 107, 107, 107, 107, 54, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13, 107, 107, 107, 107, 107] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 261 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113756 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC=CC2=CC=CN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 163, 75, 75, 75, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 75, 163, 201, 201, 201, 201, 201, 201, 201, 201, 201, 163, 75, 75, 75, 75, 13, 6, 6, 4, 4, 75, 75, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 507 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113756 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC=CC2=CC=CN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 47, 66, 74, 74, 74, 74, 13, 13, 1, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 13, 47, 47, 66, 66, 1, 1, 24, 24, 24, 24, 24] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 311 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113756 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC=CC2=CC=CN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 24, 24, 24, 107, 107, 107, 178, 201, 201, 201, 201, 201, 107, 107, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 24, 24, 24, 24, 107, 178, 178, 201, 201, 24, 24, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 650 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113756 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113756 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113756/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113756/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113756 Building REAL300020113757 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113757' /scratch/stefan/7770410/working/building/REAL300020113757 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113757 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113757/0 /scratch/stefan/7770410/working/building/REAL300020113757 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1126) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1126 `/scratch/stefan/7770410/working/3D/1126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=C2C=CC=CN2N=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113757.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113757 none O=C(CC1=C2C=CC=CN2N=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 20, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 8, 8, 8, 21, 31, 31, 31, 31, 31, 8, 8, 1, 20, 20, 48, 48, 48, 48, 48, 4, 1, 1, 1, 1, 8, 21, 21, 31, 31, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 46, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 229 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113757 none O=C(CC1=C2C=CC=CN2N=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 68, 141, 141, 141, 141, 141, 141, 141, 141, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 68, 68, 141, 141, 141, 141, 141, 15, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 377 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113757 none O=C(CC1=C2C=CC=CN2N=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 48, 48, 48, 141, 141, 141, 180, 201, 201, 201, 201, 201, 141, 141, 48, 8, 8, 1, 1, 1, 1, 1, 28, 48, 48, 48, 48, 141, 180, 180, 201, 201, 48, 48] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 618 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113757 none O=C(CC1=C2C=CC=CN2N=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 112, 201, 201, 201, 201, 201, 201, 201, 201, 32, 32, 32, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 32, 112, 112, 201, 201, 201, 201, 201, 40, 32, 32, 32, 32, 8, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 553 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113757 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113757/1 /scratch/stefan/7770410/working/building/REAL300020113757 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1127) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1127 `/scratch/stefan/7770410/working/3D/1127' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=C2C=CC=CN2N=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113757.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113757 none O=C(CC1=C2C=CC=CN2N=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 20, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 8, 8, 8, 21, 31, 31, 31, 31, 31, 8, 8, 1, 20, 20, 48, 48, 48, 48, 48, 4, 1, 1, 1, 1, 8, 21, 21, 31, 31, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 46, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 229 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113757 none O=C(CC1=C2C=CC=CN2N=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 68, 141, 141, 141, 141, 141, 141, 141, 141, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 68, 68, 141, 141, 141, 141, 141, 15, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 377 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113757 none O=C(CC1=C2C=CC=CN2N=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 48, 48, 48, 141, 141, 141, 181, 201, 201, 201, 201, 201, 141, 141, 48, 8, 8, 1, 1, 1, 1, 1, 28, 48, 48, 48, 48, 141, 181, 181, 201, 201, 48, 48] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 618 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113757 none O=C(CC1=C2C=CC=CN2N=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 111, 201, 201, 201, 201, 201, 201, 201, 201, 32, 32, 32, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 32, 111, 111, 201, 201, 201, 201, 201, 40, 32, 32, 32, 32, 8, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 548 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113757 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113757 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113757/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113757/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113757 Building REAL300020113758 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113758' /scratch/stefan/7770410/working/building/REAL300020113758 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113758 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113758/0 /scratch/stefan/7770410/working/building/REAL300020113758 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1128) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1128 `/scratch/stefan/7770410/working/3D/1128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC=CC1=CC=CC(F)=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113758.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113758 none O=C(CC=CC1=CC=CC(F)=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 15, 22, 22, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 1, 7, 7, 7, 19, 30, 30, 30, 30, 30, 7, 7, 1, 15, 15, 22, 22, 54, 54, 54, 54, 4, 1, 1, 1, 1, 7, 19, 19, 30, 30, 1, 1] 201 rigid atoms, others: [48, 38, 39, 40, 41, 12, 13, 14, 15, 16, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 245 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113758 none O=C(CC=CC1=CC=CC(F)=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 67, 75, 75, 142, 142, 142, 142, 142, 142, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 67, 67, 75, 75, 142, 142, 142, 142, 15, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 406 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113758 none O=C(CC=CC1=CC=CC(F)=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 54, 54, 54, 142, 142, 142, 177, 201, 201, 201, 201, 201, 142, 142, 54, 11, 11, 5, 5, 1, 1, 1, 1, 31, 54, 54, 54, 54, 142, 177, 177, 201, 201, 54, 54] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 36] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 644 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113758 none O=C(CC=CC1=CC=CC(F)=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 143, 153, 153, 201, 201, 201, 201, 201, 201, 32, 32, 32, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 32, 143, 143, 153, 153, 201, 201, 201, 201, 43, 32, 32, 32, 32, 8, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 660 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113758 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113758/1 /scratch/stefan/7770410/working/building/REAL300020113758 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1129) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1129 `/scratch/stefan/7770410/working/3D/1129' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC=CC1=CC=CC(F)=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113758.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113758 none O=C(CC=CC1=CC=CC(F)=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 15, 21, 21, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 1, 7, 7, 7, 18, 29, 29, 29, 29, 29, 7, 7, 1, 15, 15, 21, 21, 54, 54, 54, 54, 4, 1, 1, 1, 1, 7, 18, 18, 29, 29, 1, 1] 201 rigid atoms, others: [48, 38, 39, 40, 41, 12, 13, 14, 15, 16, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 241 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113758 none O=C(CC=CC1=CC=CC(F)=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 69, 76, 76, 140, 140, 140, 140, 140, 140, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 69, 69, 76, 76, 140, 140, 140, 140, 15, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 407 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113758 none O=C(CC=CC1=CC=CC(F)=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 54, 54, 54, 140, 140, 140, 176, 201, 201, 201, 201, 201, 140, 140, 54, 11, 11, 5, 5, 1, 1, 1, 1, 30, 54, 54, 54, 54, 140, 176, 176, 201, 201, 54, 54] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 36] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 656 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113758 none O=C(CC=CC1=CC=CC(F)=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 144, 154, 154, 201, 201, 201, 201, 201, 201, 32, 32, 32, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 32, 144, 144, 154, 154, 201, 201, 201, 201, 43, 32, 32, 32, 32, 8, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 661 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113758 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113758 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113758/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113758/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113758 Building REAL300020113759 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113759' /scratch/stefan/7770410/working/building/REAL300020113759 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113759 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113759/0 /scratch/stefan/7770410/working/building/REAL300020113759 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1130) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1130 `/scratch/stefan/7770410/working/3D/1130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C(C2CC2)O1) `REAL300020113759.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113759 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C(C2CC2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 56, 63, 63, 63, 63, 143, 143, 63, 56, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 63, 143, 143, 143, 143, 143] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 431 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113759 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C(C2CC2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 13, 16, 16, 42, 42, 42, 143, 143, 143, 187, 201, 201, 201, 201, 201, 143, 143, 42, 13, 13, 13, 1, 1, 1, 1, 13, 16, 42, 42, 42, 42, 143, 187, 187, 201, 201, 42, 42, 13, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 559 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113759 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C(C2CC2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [159, 159, 55, 55, 55, 10, 10, 10, 4, 2, 1, 1, 1, 1, 1, 1, 10, 10, 55, 159, 159, 159, 159, 159, 201, 201, 159, 159, 55, 55, 55, 55, 10, 4, 4, 2, 2, 55, 55, 159, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 586 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113759 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C(C2CC2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 35, 50, 50, 50, 50, 50, 13, 13, 1, 6, 11, 11, 11, 11, 42, 42, 11, 6, 1, 1, 1, 1, 13, 35, 35, 50, 50, 1, 1, 11, 42, 42, 42, 42, 42] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 293 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113759 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C(C2CC2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 11, 11, 11, 63, 63, 63, 122, 160, 160, 160, 160, 160, 63, 63, 11, 1, 1, 1, 1, 1, 13, 13, 1, 4, 11, 11, 11, 11, 63, 122, 122, 160, 160, 11, 11, 1, 13, 13, 13, 13, 13] 201 rigid atoms, others: [1, 39, 19, 20, 21, 22, 23, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 625 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113759 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113759/1 /scratch/stefan/7770410/working/building/REAL300020113759 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1131) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1131 `/scratch/stefan/7770410/working/3D/1131' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C(C2CC2)O1) `REAL300020113759.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113759/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113759 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C(C2CC2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 56, 63, 63, 63, 63, 143, 143, 63, 56, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 63, 143, 143, 143, 143, 143] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 431 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113759 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C(C2CC2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 13, 16, 16, 42, 42, 42, 143, 143, 143, 187, 201, 201, 201, 201, 201, 143, 143, 42, 13, 13, 13, 1, 1, 1, 1, 13, 16, 42, 42, 42, 42, 143, 187, 187, 201, 201, 42, 42, 13, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 556 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113759 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C(C2CC2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [161, 161, 56, 56, 56, 10, 10, 10, 4, 2, 1, 1, 1, 1, 1, 1, 10, 10, 56, 161, 161, 161, 161, 161, 201, 201, 161, 161, 56, 56, 56, 56, 10, 4, 4, 2, 2, 56, 56, 161, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 586 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113759 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C(C2CC2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 35, 50, 50, 50, 50, 50, 13, 13, 1, 6, 11, 11, 11, 11, 42, 42, 11, 6, 1, 1, 1, 1, 13, 35, 35, 50, 50, 1, 1, 11, 42, 42, 42, 42, 42] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 293 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113759 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C(C2CC2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 11, 11, 11, 63, 63, 63, 122, 160, 160, 160, 160, 160, 63, 63, 11, 1, 1, 1, 1, 1, 13, 13, 1, 4, 11, 11, 11, 11, 63, 122, 122, 160, 160, 11, 11, 1, 13, 13, 13, 13, 13] 201 rigid atoms, others: [1, 39, 19, 20, 21, 22, 23, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 625 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113759 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113759 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113759/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113759/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113759 Building REAL300020113760 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113760' /scratch/stefan/7770410/working/building/REAL300020113760 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113760 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113760/0 /scratch/stefan/7770410/working/building/REAL300020113760 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1132) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1132 `/scratch/stefan/7770410/working/3D/1132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C[C@@H]1NC(=O)NC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113760.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113760 none O=C(C[C@@H]1NC(=O)NC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 8, 1, 11, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 21, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 10, 10, 10, 33, 48, 59, 59, 59, 59, 10, 10, 1, 21, 21, 29, 29, 5, 1, 1, 1, 1, 10, 33, 33, 48, 48, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 42, 11, 12, 13, 14, 15, 43, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 318 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113760 none O=C(C[C@@H]1NC(=O)NC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 8, 1, 11, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 89, 104, 104, 104, 104, 104, 104, 104, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 11, 11, 11, 11, 1, 1, 10, 89, 89, 104, 104, 28, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10] 201 rigid atoms, others: [37, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 403 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113760 none O=C(C[C@@H]1NC(=O)NC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 8, 1, 11, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 29, 29, 29, 104, 104, 104, 165, 201, 201, 201, 201, 201, 104, 104, 29, 4, 4, 1, 1, 14, 29, 29, 29, 29, 104, 165, 165, 201, 201, 29, 29] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 714 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113760 none O=C(C[C@@H]1NC(=O)NC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 8, 1, 11, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 187, 201, 201, 201, 201, 201, 201, 201, 59, 59, 59, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 59, 187, 187, 201, 201, 99, 59, 59, 59, 59, 11, 6, 6, 4, 4, 59, 59] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 740 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113760 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113760/1 /scratch/stefan/7770410/working/building/REAL300020113760 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1133) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1133 `/scratch/stefan/7770410/working/3D/1133' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C[C@@H]1NC(=O)NC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113760.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113760 none O=C(C[C@@H]1NC(=O)NC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 8, 1, 11, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 21, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 10, 10, 10, 33, 48, 59, 59, 59, 59, 10, 10, 1, 21, 21, 29, 29, 5, 1, 1, 1, 1, 10, 33, 33, 48, 48, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 42, 11, 12, 13, 14, 15, 43, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 318 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113760 none O=C(C[C@@H]1NC(=O)NC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 8, 1, 11, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 89, 104, 104, 104, 104, 104, 104, 104, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 11, 11, 11, 11, 1, 1, 10, 89, 89, 104, 104, 28, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10] 201 rigid atoms, others: [37, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 403 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113760 none O=C(C[C@@H]1NC(=O)NC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 8, 1, 11, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 29, 29, 29, 104, 104, 104, 165, 201, 201, 201, 201, 201, 104, 104, 29, 4, 4, 1, 1, 14, 29, 29, 29, 29, 104, 165, 165, 201, 201, 29, 29] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 714 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113760 none O=C(C[C@@H]1NC(=O)NC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 8, 1, 11, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 187, 201, 201, 201, 201, 201, 201, 201, 58, 58, 58, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 58, 187, 187, 201, 201, 98, 58, 58, 58, 58, 11, 6, 6, 4, 4, 58, 58] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 744 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113760 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113760 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113760/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113760/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113760 Building REAL300020113761 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113761' /scratch/stefan/7770410/working/building/REAL300020113761 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113761 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113761/0 /scratch/stefan/7770410/working/building/REAL300020113761 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1134) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1134 `/scratch/stefan/7770410/working/3D/1134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020113761.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113761 none COCC1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 35, 12, 12, 12, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 21, 34, 34, 34, 34, 34, 8, 8, 1, 12, 52, 52, 52, 35, 35, 12, 12, 5, 1, 1, 1, 1, 8, 21, 21, 34, 34, 1, 1, 12] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47]) total number of confs: 286 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113761 none COCC1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 107, 46, 46, 46, 46, 46, 18, 18, 18, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 46, 127, 127, 127, 107, 107, 46, 46, 18, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8, 46] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 434 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113761 none COCC1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 46, 46, 46, 87, 114, 114, 114, 114, 114, 46, 46, 12, 1, 16, 16, 16, 7, 7, 1, 1, 5, 12, 12, 12, 12, 46, 87, 87, 114, 114, 12, 12, 1] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 34, 47, 27] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 477 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113761 none COCC1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 116, 116, 116, 116, 116, 59, 59, 59, 40, 40, 40, 10, 10, 10, 4, 2, 1, 1, 1, 1, 1, 1, 10, 10, 40, 116, 201, 201, 201, 201, 201, 116, 116, 59, 40, 40, 40, 40, 10, 4, 4, 2, 2, 40, 40, 116] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 696 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113761 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113761/1 /scratch/stefan/7770410/working/building/REAL300020113761 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1135) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1135 `/scratch/stefan/7770410/working/3D/1135' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020113761.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113761 none COCC1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 35, 12, 12, 12, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 21, 33, 33, 33, 33, 33, 8, 8, 1, 12, 52, 52, 52, 35, 35, 12, 12, 5, 1, 1, 1, 1, 8, 21, 21, 33, 33, 1, 1, 12] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47]) total number of confs: 280 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113761 none COCC1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 106, 45, 45, 45, 45, 45, 17, 17, 17, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 45, 127, 127, 127, 106, 106, 45, 45, 17, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8, 45] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 432 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113761 none COCC1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 45, 45, 45, 86, 114, 114, 114, 114, 114, 45, 45, 12, 1, 16, 16, 16, 7, 7, 1, 1, 5, 12, 12, 12, 12, 45, 86, 86, 114, 114, 12, 12, 1] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 34, 47, 27] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 482 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113761 none COCC1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 116, 116, 116, 116, 116, 59, 59, 59, 40, 40, 40, 10, 10, 10, 4, 2, 1, 1, 1, 1, 1, 1, 10, 10, 40, 116, 201, 201, 201, 201, 201, 116, 116, 59, 40, 40, 40, 40, 10, 4, 4, 2, 2, 40, 40, 116] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 697 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113761 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113761 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113761/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113761/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113761 Building REAL300020113762 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113762' /scratch/stefan/7770410/working/building/REAL300020113762 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113762 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113762/0 /scratch/stefan/7770410/working/building/REAL300020113762 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1136) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1136 `/scratch/stefan/7770410/working/3D/1136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2CCCN12) `REAL300020113762.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113762 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2CCCN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 13, 13, 13, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 13, 57, 120, 120, 120, 120, 120, 120, 120, 57, 13, 13, 13, 13, 1, 7, 7, 9, 9, 13, 13, 120, 120, 120, 120, 120, 120, 120] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 283 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113762 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2CCCN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [172, 172, 67, 67, 67, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 67, 172, 201, 201, 201, 201, 201, 201, 201, 172, 67, 67, 67, 67, 12, 6, 6, 4, 4, 67, 67, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 519 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113762 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2CCCN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 38, 56, 65, 65, 65, 65, 13, 13, 1, 6, 27, 27, 27, 27, 27, 27, 26, 6, 1, 1, 1, 1, 13, 38, 38, 56, 56, 1, 1, 27, 27, 27, 27, 27, 27, 27] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 284 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113762 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2CCCN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 27, 27, 27, 120, 120, 120, 176, 201, 201, 201, 201, 201, 120, 120, 27, 1, 1, 1, 1, 1, 1, 1, 1, 9, 27, 27, 27, 27, 120, 176, 176, 201, 201, 27, 27, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 39, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 626 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113762 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113762/1 /scratch/stefan/7770410/working/building/REAL300020113762 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1137) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1137 `/scratch/stefan/7770410/working/3D/1137' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2CCCN12) `REAL300020113762.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113762 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2CCCN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 13, 13, 13, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 13, 57, 120, 120, 120, 120, 120, 120, 120, 57, 13, 13, 13, 13, 1, 7, 7, 9, 9, 13, 13, 120, 120, 120, 120, 120, 120, 120] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 283 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113762 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2CCCN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [171, 171, 65, 65, 65, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 65, 171, 201, 201, 201, 201, 201, 201, 201, 171, 65, 65, 65, 65, 12, 6, 6, 4, 4, 65, 65, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 517 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113762 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2CCCN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 38, 56, 65, 65, 65, 65, 13, 13, 1, 6, 27, 27, 27, 27, 27, 27, 26, 6, 1, 1, 1, 1, 13, 38, 38, 56, 56, 1, 1, 27, 27, 27, 27, 27, 27, 27] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 284 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113762 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2CCCN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 27, 27, 27, 120, 120, 120, 176, 201, 201, 201, 201, 201, 120, 120, 27, 1, 1, 1, 1, 1, 1, 1, 1, 9, 27, 27, 27, 27, 120, 176, 176, 201, 201, 27, 27, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 39, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 626 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113762 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113762 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113762/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113762/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113762 Building REAL300020113763 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113763' /scratch/stefan/7770410/working/building/REAL300020113763 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113763 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113763/0 /scratch/stefan/7770410/working/building/REAL300020113763 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1138) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1138 `/scratch/stefan/7770410/working/3D/1138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=NC=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113763.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113763 none CC1=CC=NC=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 39, 39, 25, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 19, 31, 31, 31, 31, 31, 7, 7, 1, 39, 39, 39, 39, 39, 39, 25, 25, 5, 1, 1, 1, 1, 7, 19, 19, 31, 31, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 244 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113763 none CC1=CC=NC=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 120, 120, 120, 120, 91, 19, 19, 19, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 120, 120, 120, 120, 120, 120, 91, 91, 19, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 391 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113763 none CC1=CC=NC=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 20, 20, 20, 39, 39, 39, 120, 120, 120, 172, 201, 201, 201, 201, 201, 120, 120, 39, 2, 2, 2, 1, 1, 1, 5, 5, 20, 39, 39, 39, 39, 120, 172, 172, 201, 201, 39, 39] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 676 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113763 none CC1=CC=NC=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 158, 51, 51, 51, 32, 32, 32, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 32, 201, 201, 201, 201, 201, 201, 158, 158, 51, 32, 32, 32, 32, 7, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 663 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113763 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113763/1 /scratch/stefan/7770410/working/building/REAL300020113763 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1139) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1139 `/scratch/stefan/7770410/working/3D/1139' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=NC=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113763.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113763 none CC1=CC=NC=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 40, 40, 40, 26, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 20, 32, 32, 32, 32, 32, 7, 7, 1, 40, 40, 40, 40, 40, 40, 26, 26, 5, 1, 1, 1, 1, 7, 20, 20, 32, 32, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 250 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113763 none CC1=CC=NC=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 119, 119, 119, 119, 91, 19, 19, 19, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 119, 119, 119, 119, 119, 119, 91, 91, 19, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 389 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113763 none CC1=CC=NC=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 20, 20, 20, 40, 40, 40, 119, 119, 119, 172, 201, 201, 201, 201, 201, 119, 119, 40, 2, 2, 2, 1, 1, 1, 5, 5, 20, 40, 40, 40, 40, 119, 172, 172, 201, 201, 40, 40] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 678 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113763 none CC1=CC=NC=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 159, 51, 51, 51, 32, 32, 32, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 32, 201, 201, 201, 201, 201, 201, 159, 159, 51, 32, 32, 32, 32, 7, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 661 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113763 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113763 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113763/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113763/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113763 Building REAL300020113764 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113764' /scratch/stefan/7770410/working/building/REAL300020113764 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113764 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113764/0 /scratch/stefan/7770410/working/building/REAL300020113764 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1140) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1140 `/scratch/stefan/7770410/working/3D/1140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1F) `REAL300020113764.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113764 none CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 16, 18, 16, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 29, 43, 44, 44, 44, 44, 11, 11, 1, 16, 16, 16, 18, 18, 18, 18, 18, 18, 16, 16, 5, 1, 1, 1, 1, 11, 29, 29, 43, 43, 1, 1, 16] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49]) total number of confs: 206 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113764 none CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 75, 77, 75, 75, 75, 26, 26, 26, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 75, 75, 75, 77, 77, 77, 77, 77, 77, 75, 75, 26, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 75] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 178 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113764 none CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 75, 75, 75, 144, 201, 201, 201, 201, 201, 75, 75, 16, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 5, 16, 16, 16, 16, 75, 144, 144, 201, 201, 16, 16, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 49, 35, 36, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 809 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113764 none CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 72, 72, 72, 46, 46, 46, 11, 11, 11, 5, 3, 1, 1, 1, 1, 1, 1, 11, 11, 46, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 72, 46, 46, 46, 46, 11, 5, 5, 3, 3, 46, 46, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 387 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113764 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113764/1 /scratch/stefan/7770410/working/building/REAL300020113764 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1141) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1141 `/scratch/stefan/7770410/working/3D/1141' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1F) `REAL300020113764.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113764 none CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 16, 18, 16, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 29, 43, 44, 44, 44, 44, 11, 11, 1, 16, 16, 16, 18, 18, 18, 18, 18, 18, 16, 16, 5, 1, 1, 1, 1, 11, 29, 29, 43, 43, 1, 1, 16] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49]) total number of confs: 206 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113764 none CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 75, 77, 75, 75, 75, 26, 26, 26, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 75, 75, 75, 77, 77, 77, 77, 77, 77, 75, 75, 26, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 75] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 178 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113764 none CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 75, 75, 75, 144, 201, 201, 201, 201, 201, 75, 75, 16, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 5, 16, 16, 16, 16, 75, 144, 144, 201, 201, 16, 16, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 49, 35, 36, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 809 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113764 none CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 71, 71, 71, 45, 45, 45, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 45, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 71, 45, 45, 45, 45, 10, 5, 5, 3, 3, 45, 45, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 389 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113764 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113764 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113764/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113764/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113764 Building REAL300020113765 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113765' /scratch/stefan/7770410/working/building/REAL300020113765 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113765 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113765/0 /scratch/stefan/7770410/working/building/REAL300020113765 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1142) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1142 `/scratch/stefan/7770410/working/3D/1142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2NC(=O)OC2=C1) `REAL300020113765.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113765 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2NC(=O)OC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 11, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 25, 73, 73, 73, 73, 73, 73, 73, 73, 73, 25, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 73, 73, 73, 73] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 169 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113765 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2NC(=O)OC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 11, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 49, 49, 49, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 49, 85, 201, 201, 201, 201, 201, 201, 201, 201, 201, 85, 49, 49, 49, 49, 10, 6, 6, 4, 4, 49, 49, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 417 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113765 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2NC(=O)OC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 11, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 31, 45, 49, 49, 49, 49, 9, 9, 1, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 9, 31, 31, 45, 45, 1, 1, 13, 13, 13, 13] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113765 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2NC(=O)OC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 11, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 13, 13, 13, 73, 73, 73, 146, 201, 201, 201, 201, 201, 73, 73, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 13, 73, 146, 146, 201, 201, 13, 13, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 812 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113765 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113765/1 /scratch/stefan/7770410/working/building/REAL300020113765 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1143) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1143 `/scratch/stefan/7770410/working/3D/1143' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2NC(=O)OC2=C1) `REAL300020113765.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113765/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113765 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2NC(=O)OC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 11, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 25, 73, 73, 73, 73, 73, 73, 73, 73, 73, 25, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 73, 73, 73, 73] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 169 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113765 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2NC(=O)OC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 11, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 49, 49, 49, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 49, 85, 201, 201, 201, 201, 201, 201, 201, 201, 201, 85, 49, 49, 49, 49, 10, 6, 6, 4, 4, 49, 49, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 417 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113765 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2NC(=O)OC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 11, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 31, 45, 49, 49, 49, 49, 9, 9, 1, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 9, 31, 31, 45, 45, 1, 1, 13, 13, 13, 13] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113765 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2NC(=O)OC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 11, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 13, 13, 13, 73, 73, 73, 146, 201, 201, 201, 201, 201, 73, 73, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 13, 73, 146, 146, 201, 201, 13, 13, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 812 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113765 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113765 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113765/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113765/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113765 Building REAL300020113766 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113766' /scratch/stefan/7770410/working/building/REAL300020113766 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113766 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113766/0 /scratch/stefan/7770410/working/building/REAL300020113766 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1144) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1144 `/scratch/stefan/7770410/working/3D/1144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCC1=O) `REAL300020113766.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113766 none CN1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 49, 55, 55, 55, 55, 11, 11, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 11, 33, 33, 49, 49, 1, 1, 23, 23, 23, 23] 201 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 43, 44, 22] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48]) total number of confs: 266 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113766 none CN1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 34, 34, 34, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 104, 104, 104, 104, 104, 104, 104, 104, 104, 104, 34, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 104, 104, 104, 104] 201 rigid atoms, others: [38, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 308 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113766 none CN1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 8, 23, 23, 23, 104, 104, 104, 165, 201, 201, 201, 201, 201, 104, 104, 23, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 9, 23, 23, 23, 23, 104, 165, 165, 201, 201, 23, 23, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 32, 45, 46, 47, 48, 23, 24, 25, 26, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 706 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113766 none CN1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 104, 104, 104, 57, 57, 57, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 57, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 104, 57, 57, 57, 57, 12, 6, 6, 4, 4, 57, 57, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 598 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113766 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113766/1 /scratch/stefan/7770410/working/building/REAL300020113766 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1145) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1145 `/scratch/stefan/7770410/working/3D/1145' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC1=O) `REAL300020113766.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113766/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113766 none CN1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 49, 55, 55, 55, 55, 11, 11, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 11, 33, 33, 49, 49, 1, 1, 23, 23, 23, 23] 201 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 43, 44, 22] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48]) total number of confs: 266 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113766 none CN1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 34, 34, 34, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 103, 103, 103, 103, 103, 103, 103, 103, 103, 103, 34, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 103, 103, 103, 103] 201 rigid atoms, others: [38, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 306 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113766 none CN1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 8, 23, 23, 23, 103, 103, 103, 165, 201, 201, 201, 201, 201, 103, 103, 23, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 9, 23, 23, 23, 23, 103, 165, 165, 201, 201, 23, 23, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 32, 45, 46, 47, 48, 23, 24, 25, 26, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 711 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113766 none CN1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 104, 104, 104, 56, 56, 56, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 56, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 104, 56, 56, 56, 56, 11, 6, 6, 4, 4, 56, 56, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 599 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113766 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113766 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113766/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113766/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113766 Building REAL300020113767 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113767' /scratch/stefan/7770410/working/building/REAL300020113767 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113767 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113767/0 /scratch/stefan/7770410/working/building/REAL300020113767 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1146) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1146 `/scratch/stefan/7770410/working/3D/1146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020113767.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113767 none COC1=CC=CC(C(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 30, 30, 30, 30, 30, 13, 6, 13, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 29, 42, 43, 43, 43, 43, 9, 9, 1, 30, 40, 40, 40, 30, 30, 30, 13, 13, 13, 13, 6, 1, 1, 1, 1, 9, 29, 29, 42, 42, 1, 1, 30] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 51]) total number of confs: 262 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113767 none COC1=CC=CC(C(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 93, 93, 93, 93, 93, 49, 25, 49, 25, 25, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 10, 10, 10, 10, 1, 1, 9, 93, 113, 113, 113, 93, 93, 93, 49, 49, 49, 49, 25, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9, 93] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 329 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113767 none COC1=CC=CC(C(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 12, 12, 30, 30, 30, 93, 93, 93, 163, 200, 201, 201, 201, 201, 93, 93, 30, 1, 3, 3, 3, 1, 1, 1, 4, 4, 4, 4, 12, 30, 30, 30, 30, 93, 163, 163, 200, 200, 30, 30, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 51, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 751 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113767 none COC1=CC=CC(C(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 128, 81, 128, 81, 81, 45, 45, 45, 12, 12, 12, 5, 3, 1, 1, 1, 1, 1, 1, 12, 12, 45, 201, 201, 201, 201, 201, 201, 201, 128, 128, 128, 128, 81, 45, 45, 45, 45, 12, 5, 5, 3, 3, 45, 45, 201] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 603 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113767 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113767/1 /scratch/stefan/7770410/working/building/REAL300020113767 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1147) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1147 `/scratch/stefan/7770410/working/3D/1147' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020113767.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113767/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113767 none COC1=CC=CC(C(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 30, 30, 30, 30, 30, 13, 6, 13, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 28, 41, 42, 42, 42, 42, 9, 9, 1, 30, 40, 40, 40, 30, 30, 30, 13, 13, 13, 13, 6, 1, 1, 1, 1, 9, 28, 28, 41, 41, 1, 1, 30] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 51]) total number of confs: 259 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113767 none COC1=CC=CC(C(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 94, 94, 94, 94, 94, 49, 25, 49, 25, 25, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 9, 94, 114, 114, 114, 94, 94, 94, 49, 49, 49, 49, 25, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 94] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 328 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113767 none COC1=CC=CC(C(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 12, 12, 30, 30, 30, 94, 94, 94, 163, 200, 201, 201, 201, 201, 94, 94, 30, 1, 3, 3, 3, 1, 1, 1, 4, 4, 4, 4, 12, 30, 30, 30, 30, 94, 163, 163, 200, 200, 30, 30, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 51, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 749 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113767 none COC1=CC=CC(C(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 127, 79, 127, 79, 79, 43, 43, 43, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 43, 201, 201, 201, 201, 201, 201, 201, 127, 127, 127, 127, 79, 43, 43, 43, 43, 10, 5, 5, 3, 3, 43, 43, 201] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 609 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113767 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113767 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113767/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113767/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113767 Building REAL300020113768 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113768' /scratch/stefan/7770410/working/building/REAL300020113768 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113768 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113768/0 /scratch/stefan/7770410/working/building/REAL300020113768 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1148) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1148 `/scratch/stefan/7770410/working/3D/1148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113768.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113768 none CCOCCOCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 120, 98, 61, 46, 17, 17, 17, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 128, 128, 128, 128, 128, 120, 120, 98, 98, 46, 46, 17, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 564 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113768 none CCOCCOCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 163, 93, 78, 34, 34, 34, 26, 26, 26, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 26, 201, 201, 201, 201, 201, 201, 201, 163, 163, 78, 78, 34, 26, 26, 26, 26, 7, 4, 4, 2, 2, 26, 26] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 927 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113768 none CCOCCOCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 54, 40, 24, 15, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 19, 30, 30, 30, 30, 30, 7, 7, 1, 64, 64, 64, 64, 64, 54, 54, 40, 40, 15, 15, 5, 1, 1, 1, 1, 7, 19, 19, 30, 30, 1, 1] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 364 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113768 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113768/1 /scratch/stefan/7770410/working/building/REAL300020113768 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1149) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1149 `/scratch/stefan/7770410/working/3D/1149' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113768.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113768/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113768 none CCOCCOCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [129, 129, 120, 98, 60, 45, 17, 17, 17, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 129, 129, 129, 129, 129, 120, 120, 98, 98, 45, 45, 17, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 566 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113768 none CCOCCOCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 165, 94, 79, 34, 34, 34, 27, 27, 27, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 27, 201, 201, 201, 201, 201, 201, 201, 165, 165, 79, 79, 34, 27, 27, 27, 27, 8, 4, 4, 2, 2, 27, 27] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 921 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113768 none CCOCCOCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 53, 40, 24, 15, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 19, 30, 30, 30, 30, 30, 7, 7, 1, 63, 63, 63, 63, 63, 53, 53, 40, 40, 15, 15, 5, 1, 1, 1, 1, 7, 19, 19, 30, 30, 1, 1] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 358 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113768 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113768 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113768/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113768/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113768 Building REAL300020113769 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113769' /scratch/stefan/7770410/working/building/REAL300020113769 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113769 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113769/0 /scratch/stefan/7770410/working/building/REAL300020113769 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1150) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1150 `/scratch/stefan/7770410/working/3D/1150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC(C1CC1)C1CC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113769.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113769 none O=C(CC(C1CC1)C1CC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 12, 4, 1, 4, 9, 9, 1, 1, 1, 29, 29, 63, 63, 63, 110, 110, 110, 171, 200, 200, 200, 200, 200, 110, 110, 63, 12, 12, 4, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 29, 63, 63, 63, 63, 110, 171, 171, 200, 200, 63, 63] 201 rigid atoms, others: [3, 36, 37, 38, 7, 8, 9, 39, 35] set([0, 1, 2, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 762 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113769 none O=C(CC(C1CC1)C1CC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 184, 199, 201, 201, 200, 200, 200, 40, 40, 40, 16, 16, 16, 7, 4, 1, 1, 1, 1, 1, 1, 16, 16, 40, 184, 184, 200, 201, 201, 201, 201, 201, 200, 200, 200, 200, 200, 69, 40, 40, 40, 40, 16, 7, 7, 4, 4, 40, 40] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 753 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113769 none O=C(CC(C1CC1)C1CC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 34, 58, 63, 63, 60, 63, 63, 1, 1, 1, 1, 1, 6, 6, 6, 24, 33, 40, 40, 40, 40, 6, 6, 1, 34, 34, 60, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 6, 1, 1, 1, 1, 6, 24, 24, 33, 33, 1, 1] 201 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 44, 50, 51, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 411 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113769 none O=C(CC(C1CC1)C1CC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 14, 5, 1, 1, 1, 1, 5, 9, 9, 31, 31, 63, 63, 63, 112, 112, 112, 172, 201, 201, 201, 201, 201, 112, 112, 63, 14, 14, 5, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 31, 63, 63, 63, 63, 112, 172, 172, 201, 201, 63, 63] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 30, 31] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 767 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113769 none O=C(CC(C1CC1)C1CC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 87, 109, 112, 112, 110, 110, 110, 6, 6, 6, 1, 1, 1, 1, 1, 8, 11, 15, 15, 15, 15, 1, 1, 6, 87, 87, 110, 112, 112, 112, 112, 112, 110, 110, 110, 110, 110, 21, 6, 6, 6, 6, 1, 8, 8, 11, 11, 6, 6] 201 rigid atoms, others: [45, 14, 13, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 487 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113769 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113769/1 /scratch/stefan/7770410/working/building/REAL300020113769 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1151) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1151 `/scratch/stefan/7770410/working/3D/1151' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC(C1CC1)C1CC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113769.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113769 none O=C(CC(C1CC1)C1CC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 12, 4, 1, 4, 9, 9, 1, 1, 1, 29, 29, 65, 65, 65, 112, 112, 112, 172, 200, 200, 200, 200, 200, 112, 112, 65, 12, 12, 4, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 29, 65, 65, 65, 65, 112, 172, 172, 200, 200, 65, 65] 201 rigid atoms, others: [3, 36, 37, 38, 7, 8, 9, 39, 35] set([0, 1, 2, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 754 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113769 none O=C(CC(C1CC1)C1CC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 185, 199, 201, 201, 200, 200, 200, 39, 39, 39, 15, 15, 15, 7, 4, 1, 1, 1, 1, 1, 1, 15, 15, 39, 185, 185, 200, 201, 201, 201, 201, 201, 200, 200, 200, 200, 200, 68, 39, 39, 39, 39, 15, 7, 7, 4, 4, 39, 39] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 751 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113769 none O=C(CC(C1CC1)C1CC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 36, 60, 65, 65, 62, 65, 65, 1, 1, 1, 1, 1, 6, 6, 6, 24, 33, 40, 40, 40, 40, 6, 6, 1, 36, 36, 62, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 6, 1, 1, 1, 1, 6, 24, 24, 33, 33, 1, 1] 201 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 44, 50, 51, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 420 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113769 none O=C(CC(C1CC1)C1CC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 14, 5, 1, 1, 1, 1, 5, 9, 9, 31, 31, 65, 65, 65, 114, 114, 114, 173, 201, 201, 201, 201, 201, 114, 114, 65, 14, 14, 5, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 31, 65, 65, 65, 65, 114, 173, 173, 201, 201, 65, 65] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 30, 31] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 761 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113769 none O=C(CC(C1CC1)C1CC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 89, 111, 114, 114, 112, 112, 112, 6, 6, 6, 1, 1, 1, 1, 1, 8, 11, 15, 15, 15, 15, 1, 1, 6, 89, 89, 112, 114, 114, 114, 114, 114, 112, 112, 112, 112, 112, 21, 6, 6, 6, 6, 1, 8, 8, 11, 11, 6, 6] 201 rigid atoms, others: [45, 14, 13, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 493 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113769 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113769 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113769/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113769/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113769 Building REAL300020113770 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113770' /scratch/stefan/7770410/working/building/REAL300020113770 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113770 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113770/0 /scratch/stefan/7770410/working/building/REAL300020113770 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1152) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1152 `/scratch/stefan/7770410/working/3D/1152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC1) `REAL300020113770.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113770 none CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 86, 23, 23, 23, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 8, 8, 8, 8, 1, 1, 8, 106, 106, 106, 106, 106, 106, 106, 86, 86, 23, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8, 106, 106, 106, 106, 106] 201 rigid atoms, others: [36, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 439 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113770 none CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 182, 64, 64, 64, 36, 36, 36, 8, 8, 8, 5, 3, 1, 1, 1, 1, 1, 1, 8, 8, 36, 201, 201, 201, 201, 201, 201, 201, 182, 182, 64, 36, 36, 36, 36, 8, 5, 5, 3, 3, 36, 36, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 782 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113770 none CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 22, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 36, 36, 36, 36, 8, 8, 1, 32, 32, 32, 32, 32, 32, 32, 22, 22, 6, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1, 32, 32, 32, 32, 32] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 42, 21, 41] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113770 none CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 6, 17, 17, 17, 32, 32, 32, 106, 106, 106, 161, 201, 201, 201, 201, 201, 106, 106, 32, 1, 1, 1, 3, 3, 3, 2, 6, 6, 17, 32, 32, 32, 32, 106, 161, 161, 201, 201, 32, 32, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 43, 44, 45, 46, 47, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 732 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113770 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113770/1 /scratch/stefan/7770410/working/building/REAL300020113770 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1153) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1153 `/scratch/stefan/7770410/working/3D/1153' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC1) `REAL300020113770.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113770 none CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 87, 23, 23, 23, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 8, 8, 8, 8, 1, 1, 8, 106, 106, 106, 106, 106, 106, 106, 87, 87, 23, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8, 106, 106, 106, 106, 106] 201 rigid atoms, others: [36, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 439 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113770 none CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 182, 64, 64, 64, 36, 36, 36, 8, 8, 8, 5, 3, 1, 1, 1, 1, 1, 1, 8, 8, 36, 201, 201, 201, 201, 201, 201, 201, 182, 182, 64, 36, 36, 36, 36, 8, 5, 5, 3, 3, 36, 36, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 785 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113770 none CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 23, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 36, 36, 36, 36, 8, 8, 1, 33, 33, 33, 33, 33, 33, 33, 23, 23, 6, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1, 33, 33, 33, 33, 33] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 42, 21, 41] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47]) total number of confs: 281 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113770 none CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 6, 17, 17, 17, 33, 33, 33, 106, 106, 106, 161, 201, 201, 201, 201, 201, 106, 106, 33, 1, 1, 1, 3, 3, 3, 2, 6, 6, 17, 33, 33, 33, 33, 106, 161, 161, 201, 201, 33, 33, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 43, 44, 45, 46, 47, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 735 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113770 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113770 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113770/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113770/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113770 Building REAL300020113771 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113771' /scratch/stefan/7770410/working/building/REAL300020113771 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113771 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113771/0 /scratch/stefan/7770410/working/building/REAL300020113771 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1154) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1154 `/scratch/stefan/7770410/working/3D/1154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C2OC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CC2=CC=C1) `REAL300020113771.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113771 none CC1=C2OC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 60, 79, 97, 97, 97, 97, 13, 13, 1, 14, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 13, 60, 60, 79, 79, 1, 1, 14, 14, 14, 14] 201 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 363 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113771 none CC1=C2OC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 89, 52, 52, 52, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 13, 89, 89, 89, 89, 89, 89, 89, 89, 52, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13, 89, 89, 89, 89] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 238 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113771 none CC1=C2OC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 89, 89, 89, 161, 201, 201, 201, 201, 201, 89, 89, 14, 1, 1, 1, 1, 1, 2, 2, 2, 4, 14, 14, 14, 14, 89, 161, 161, 201, 201, 14, 14, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 45, 46, 47, 24, 25, 26, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 730 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113771 none CC1=C2OC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 182, 182, 182, 97, 97, 97, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 97, 201, 201, 201, 201, 201, 201, 201, 201, 182, 97, 97, 97, 97, 18, 6, 6, 4, 4, 97, 97, 201, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 532 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113771 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113771/1 /scratch/stefan/7770410/working/building/REAL300020113771 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1155) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1155 `/scratch/stefan/7770410/working/3D/1155' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C2OC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CC2=CC=C1) `REAL300020113771.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113771 none CC1=C2OC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 60, 79, 97, 97, 97, 97, 13, 13, 1, 14, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 13, 60, 60, 79, 79, 1, 1, 14, 14, 14, 14] 201 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 363 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113771 none CC1=C2OC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 89, 52, 52, 52, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 13, 89, 89, 89, 89, 89, 89, 89, 89, 52, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13, 89, 89, 89, 89] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 238 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113771 none CC1=C2OC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 89, 89, 89, 161, 201, 201, 201, 201, 201, 89, 89, 14, 1, 1, 1, 1, 1, 2, 2, 2, 4, 14, 14, 14, 14, 89, 161, 161, 201, 201, 14, 14, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 45, 46, 47, 24, 25, 26, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 730 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113771 none CC1=C2OC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 183, 183, 183, 97, 97, 97, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 97, 201, 201, 201, 201, 201, 201, 201, 201, 183, 97, 97, 97, 97, 18, 6, 6, 4, 4, 97, 97, 201, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 534 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113771 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113771 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113771/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113771/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113771 Building REAL300020113772 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113772' /scratch/stefan/7770410/working/building/REAL300020113772 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113772 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113772/0 /scratch/stefan/7770410/working/building/REAL300020113772 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1156) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1156 `/scratch/stefan/7770410/working/3D/1156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CSC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020113772.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113772 none NC(=O)C1=CSC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 33, 46, 33, 33, 33, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 33, 44, 57, 57, 57, 57, 8, 8, 1, 33, 46, 46, 33, 6, 1, 1, 1, 1, 8, 33, 33, 44, 44, 1, 1, 33] 201 rigid atoms, others: [32, 33, 34, 40, 9, 10, 11, 12, 13, 41, 25, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 42]) total number of confs: 287 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113772 none NC(=O)C1=CSC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 78, 101, 78, 78, 78, 26, 26, 26, 8, 8, 8, 1, 1, 1, 1, 1, 8, 12, 17, 17, 17, 17, 1, 1, 8, 78, 101, 101, 78, 26, 8, 8, 8, 8, 1, 8, 8, 12, 12, 8, 8, 78] 201 rigid atoms, others: [35, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 283 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113772 none NC(=O)C1=CSC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 12, 12, 12, 33, 33, 33, 78, 78, 78, 149, 168, 172, 172, 172, 172, 78, 78, 33, 1, 3, 3, 1, 12, 33, 33, 33, 33, 78, 149, 149, 168, 168, 33, 33, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 42, 26, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 604 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113772 none NC(=O)C1=CSC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 174, 201, 174, 174, 174, 128, 128, 128, 63, 63, 63, 25, 25, 25, 7, 4, 1, 1, 1, 1, 1, 1, 25, 25, 63, 174, 201, 201, 174, 128, 63, 63, 63, 63, 25, 7, 7, 4, 4, 63, 63, 174] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 551 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113772 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113772/1 /scratch/stefan/7770410/working/building/REAL300020113772 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1157) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1157 `/scratch/stefan/7770410/working/3D/1157' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CSC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020113772.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113772 none NC(=O)C1=CSC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 33, 46, 33, 33, 33, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 33, 44, 57, 57, 57, 57, 8, 8, 1, 33, 46, 46, 33, 6, 1, 1, 1, 1, 8, 33, 33, 44, 44, 1, 1, 33] 201 rigid atoms, others: [32, 33, 34, 40, 9, 10, 11, 12, 13, 41, 25, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 42]) total number of confs: 287 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113772 none NC(=O)C1=CSC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 78, 101, 78, 78, 78, 26, 26, 26, 8, 8, 8, 1, 1, 1, 1, 1, 8, 12, 17, 17, 17, 17, 1, 1, 8, 78, 101, 101, 78, 26, 8, 8, 8, 8, 1, 8, 8, 12, 12, 8, 8, 78] 201 rigid atoms, others: [35, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 283 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113772 none NC(=O)C1=CSC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 12, 12, 12, 33, 33, 33, 78, 78, 78, 149, 168, 172, 172, 172, 172, 78, 78, 33, 1, 3, 3, 1, 12, 33, 33, 33, 33, 78, 149, 149, 168, 168, 33, 33, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 42, 26, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 604 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113772 none NC(=O)C1=CSC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 174, 201, 174, 174, 174, 128, 128, 128, 63, 63, 63, 25, 25, 25, 7, 4, 1, 1, 1, 1, 1, 1, 25, 25, 63, 174, 201, 201, 174, 128, 63, 63, 63, 63, 25, 7, 7, 4, 4, 63, 63, 174] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 551 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113772 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113772 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113772/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113772/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113772 Building REAL300020113773 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113773' /scratch/stefan/7770410/working/building/REAL300020113773 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113773 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113773/0 /scratch/stefan/7770410/working/building/REAL300020113773 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1158) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1158 `/scratch/stefan/7770410/working/3D/1158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2CCCCC2C1) `REAL300020113773.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113773 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2CCCCC2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 58, 115, 115, 115, 115, 115, 115, 115, 115, 115, 58, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 379 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113773 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2CCCCC2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 46, 46, 46, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 46, 118, 201, 201, 201, 201, 201, 201, 201, 201, 201, 118, 46, 46, 46, 46, 9, 4, 4, 2, 2, 46, 46, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 635 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113773 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2CCCCC2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 34, 46, 46, 46, 46, 46, 13, 13, 1, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 34, 34, 46, 46, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113773 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2CCCCC2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 16, 16, 16, 115, 115, 115, 170, 201, 201, 201, 201, 201, 115, 115, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 16, 16, 16, 16, 115, 170, 170, 201, 201, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 633 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113773 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113773/1 /scratch/stefan/7770410/working/building/REAL300020113773 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1159) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1159 `/scratch/stefan/7770410/working/3D/1159' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2CCCCC2C1) `REAL300020113773.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113773 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2CCCCC2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 58, 115, 115, 115, 115, 115, 115, 115, 115, 115, 58, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 379 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113773 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2CCCCC2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 117, 45, 45, 45, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 45, 117, 201, 201, 201, 201, 201, 201, 201, 201, 201, 117, 45, 45, 45, 45, 9, 4, 4, 2, 2, 45, 45, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 637 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113773 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2CCCCC2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 34, 45, 45, 45, 45, 45, 13, 13, 1, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 34, 34, 45, 45, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113773 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2CCCCC2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 16, 16, 16, 115, 115, 115, 170, 201, 201, 201, 201, 201, 115, 115, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 16, 16, 16, 16, 115, 170, 170, 201, 201, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 633 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113773 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113773 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113773/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113773/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113773 Building REAL300020113774 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113774' /scratch/stefan/7770410/working/building/REAL300020113774 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113774 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113774/0 /scratch/stefan/7770410/working/building/REAL300020113774 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1160) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1160 `/scratch/stefan/7770410/working/3D/1160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN=C1) `REAL300020113774.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113774 none CN(C)C(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 37, 37, 37, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 52, 92, 92, 92, 92, 92, 52, 52, 52, 52, 52, 52, 52, 37, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 92, 92, 92, 92] 201 rigid atoms, others: [9, 10, 11, 12, 13, 20, 21, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 297 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113774 none CN(C)C(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 133, 104, 104, 104, 53, 53, 53, 13, 13, 13, 4, 4, 1, 1, 1, 1, 1, 1, 13, 13, 53, 133, 201, 201, 201, 201, 201, 133, 133, 133, 133, 133, 133, 133, 104, 53, 53, 53, 53, 13, 4, 4, 4, 4, 53, 53, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 586 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113774 none CN(C)C(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 35, 49, 54, 54, 54, 54, 11, 11, 1, 11, 19, 19, 19, 19, 19, 11, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 11, 35, 35, 49, 49, 1, 1, 19, 19, 19, 19] 201 rigid atoms, others: [37, 6, 7, 8, 9, 10, 39, 46, 47, 40, 22, 38] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113774 none CN(C)C(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 5, 6, 6, 6, 19, 19, 19, 92, 92, 92, 167, 201, 201, 201, 201, 201, 92, 92, 19, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 6, 19, 19, 19, 19, 92, 167, 167, 201, 201, 19, 19, 1, 1, 1, 1] 201 rigid atoms, others: [3, 48, 49, 50, 51, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 746 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113774 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113774/1 /scratch/stefan/7770410/working/building/REAL300020113774 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1161) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1161 `/scratch/stefan/7770410/working/3D/1161' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN=C1) `REAL300020113774.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113774 none CN(C)C(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 37, 37, 37, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 52, 91, 91, 91, 91, 91, 52, 52, 52, 52, 52, 52, 52, 37, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 91, 91, 91, 91] 201 rigid atoms, others: [9, 10, 11, 12, 13, 20, 21, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 295 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113774 none CN(C)C(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 133, 104, 104, 104, 53, 53, 53, 13, 13, 13, 4, 4, 1, 1, 1, 1, 1, 1, 13, 13, 53, 133, 201, 201, 201, 201, 201, 133, 133, 133, 133, 133, 133, 133, 104, 53, 53, 53, 53, 13, 4, 4, 4, 4, 53, 53, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 586 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113774 none CN(C)C(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 36, 50, 55, 55, 55, 55, 11, 11, 1, 11, 19, 19, 19, 19, 19, 11, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 11, 36, 36, 50, 50, 1, 1, 19, 19, 19, 19] 201 rigid atoms, others: [37, 6, 7, 8, 9, 10, 39, 46, 47, 40, 22, 38] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113774 none CN(C)C(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 5, 6, 6, 6, 19, 19, 19, 91, 91, 91, 167, 201, 201, 201, 201, 201, 91, 91, 19, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 6, 19, 19, 19, 19, 91, 167, 167, 201, 201, 19, 19, 1, 1, 1, 1] 201 rigid atoms, others: [3, 48, 49, 50, 51, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 748 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113774 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113774 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113774/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113774/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113774 Building REAL300020113775 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113775' /scratch/stefan/7770410/working/building/REAL300020113775 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113775 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113775/0 /scratch/stefan/7770410/working/building/REAL300020113775 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1162) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1162 `/scratch/stefan/7770410/working/3D/1162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113775.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113775 none CCCCS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 106, 96, 81, 96, 96, 28, 28, 28, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 8, 8, 8, 8, 1, 1, 8, 108, 108, 108, 108, 108, 108, 108, 106, 106, 81, 81, 28, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 469 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113775 none CCCCS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 200, 195, 192, 195, 195, 92, 92, 92, 36, 36, 36, 8, 8, 8, 5, 3, 1, 1, 1, 1, 1, 1, 8, 8, 36, 201, 201, 201, 201, 201, 201, 201, 200, 200, 192, 192, 92, 36, 36, 36, 36, 8, 5, 5, 3, 3, 36, 36] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 781 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113775 none CCCCS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 38, 29, 20, 29, 29, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 24, 36, 37, 37, 37, 37, 8, 8, 1, 40, 40, 40, 40, 40, 40, 40, 38, 38, 20, 20, 6, 1, 1, 1, 1, 8, 24, 24, 36, 36, 1, 1] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 332 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113775 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113775/1 /scratch/stefan/7770410/working/building/REAL300020113775 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1163) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1163 `/scratch/stefan/7770410/working/3D/1163' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113775.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113775/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113775 none CCCCS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 106, 96, 81, 96, 96, 28, 28, 28, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 8, 8, 8, 8, 1, 1, 8, 108, 108, 108, 108, 108, 108, 108, 106, 106, 81, 81, 28, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 469 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113775 none CCCCS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 200, 195, 191, 195, 195, 92, 92, 92, 36, 36, 36, 8, 8, 8, 5, 3, 1, 1, 1, 1, 1, 1, 8, 8, 36, 201, 201, 201, 201, 201, 201, 201, 200, 200, 191, 191, 92, 36, 36, 36, 36, 8, 5, 5, 3, 3, 36, 36] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 784 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113775 none CCCCS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 38, 29, 20, 29, 29, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 24, 36, 37, 37, 37, 37, 8, 8, 1, 40, 40, 40, 40, 40, 40, 40, 38, 38, 20, 20, 6, 1, 1, 1, 1, 8, 24, 24, 36, 36, 1, 1] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 332 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113775 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113775 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113775/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113775/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113775 Building REAL300020113776 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113776' /scratch/stefan/7770410/working/building/REAL300020113776 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113776 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113776/0 /scratch/stefan/7770410/working/building/REAL300020113776 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1164) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1164 `/scratch/stefan/7770410/working/3D/1164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2CCC1CC2) `REAL300020113776.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113776 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2CCC1CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 14, 14, 14, 14, 1, 1, 13, 56, 104, 104, 104, 104, 104, 104, 104, 56, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13, 104, 104, 104, 104, 104, 104, 104, 104, 104, 104, 104, 104, 104] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 343 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113776 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2CCC1CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [182, 182, 78, 78, 78, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 78, 182, 201, 201, 201, 201, 201, 201, 201, 182, 78, 78, 78, 78, 15, 6, 6, 4, 4, 78, 78, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 577 number of broken/clashed sets: 13 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113776 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2CCC1CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 43, 63, 77, 77, 77, 77, 13, 13, 1, 6, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 13, 43, 43, 63, 63, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 339 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113776 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2CCC1CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 22, 22, 22, 104, 104, 104, 175, 201, 201, 201, 201, 201, 104, 104, 22, 1, 1, 1, 1, 1, 1, 1, 1, 6, 22, 22, 22, 22, 104, 175, 175, 201, 201, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 678 number of broken/clashed sets: 14 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113776 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113776/1 /scratch/stefan/7770410/working/building/REAL300020113776 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1165) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1165 `/scratch/stefan/7770410/working/3D/1165' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2CCC1CC2) `REAL300020113776.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113776/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113776 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2CCC1CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 14, 14, 14, 14, 1, 1, 13, 56, 104, 104, 104, 104, 104, 104, 104, 56, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13, 104, 104, 104, 104, 104, 104, 104, 104, 104, 104, 104, 104, 104] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 343 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113776 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2CCC1CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [182, 182, 77, 77, 77, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 77, 182, 201, 201, 201, 201, 201, 201, 201, 182, 77, 77, 77, 77, 14, 6, 6, 4, 4, 77, 77, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 578 number of broken/clashed sets: 13 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113776 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2CCC1CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 43, 63, 77, 77, 77, 77, 13, 13, 1, 6, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 13, 43, 43, 63, 63, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 339 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113776 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2CCC1CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 22, 22, 22, 104, 104, 104, 175, 201, 201, 201, 201, 201, 104, 104, 22, 1, 1, 1, 1, 1, 1, 1, 1, 6, 22, 22, 22, 22, 104, 175, 175, 201, 201, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 675 number of broken/clashed sets: 14 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113776 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113776 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113776/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113776/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113776 Building REAL300020113777 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113777' /scratch/stefan/7770410/working/building/REAL300020113777 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113777 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113777/0 /scratch/stefan/7770410/working/building/REAL300020113777 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1166) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1166 `/scratch/stefan/7770410/working/3D/1166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=CC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020113777.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113777 none CCOC1=CC=CC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 22, 22, 22, 22, 22, 11, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 21, 33, 33, 33, 33, 33, 7, 7, 1, 22, 44, 44, 44, 44, 44, 22, 22, 22, 11, 11, 5, 1, 1, 1, 1, 7, 21, 21, 33, 33, 1, 1, 22] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 51]) total number of confs: 229 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113777 none CCOC1=CC=CC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 87, 87, 87, 87, 87, 52, 19, 19, 19, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 87, 128, 128, 128, 128, 128, 87, 87, 87, 52, 52, 19, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 87] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 348 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113777 none CCOC1=CC=CC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 10, 10, 10, 22, 22, 22, 87, 87, 87, 135, 174, 174, 174, 174, 174, 87, 87, 22, 1, 5, 5, 5, 5, 5, 1, 1, 1, 3, 3, 10, 22, 22, 22, 22, 87, 135, 135, 174, 174, 22, 22, 1] 201 rigid atoms, others: [51, 34, 3, 4, 5, 6, 7, 8, 2, 35, 36, 28] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 624 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113777 none CCOC1=CC=CC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 176, 176, 176, 176, 176, 108, 50, 50, 50, 34, 34, 34, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 34, 176, 201, 201, 201, 201, 201, 176, 176, 176, 108, 108, 50, 34, 34, 34, 34, 8, 4, 4, 2, 2, 34, 34, 176] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 588 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113777 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113777/1 /scratch/stefan/7770410/working/building/REAL300020113777 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1167) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1167 `/scratch/stefan/7770410/working/3D/1167' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=CC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020113777.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113777 none CCOC1=CC=CC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 22, 22, 22, 22, 22, 11, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 21, 33, 33, 33, 33, 33, 7, 7, 1, 22, 43, 43, 43, 43, 43, 22, 22, 22, 11, 11, 5, 1, 1, 1, 1, 7, 21, 21, 33, 33, 1, 1, 22] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 51]) total number of confs: 228 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113777 none CCOC1=CC=CC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [126, 126, 87, 87, 87, 87, 87, 52, 19, 19, 19, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 87, 126, 126, 126, 126, 126, 87, 87, 87, 52, 52, 19, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 87] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 345 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113777 none CCOC1=CC=CC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 10, 10, 10, 22, 22, 22, 87, 87, 87, 135, 175, 175, 175, 175, 175, 87, 87, 22, 1, 5, 5, 5, 5, 5, 1, 1, 1, 3, 3, 10, 22, 22, 22, 22, 87, 135, 135, 175, 175, 22, 22, 1] 201 rigid atoms, others: [51, 34, 3, 4, 5, 6, 7, 8, 2, 35, 36, 28] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 633 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113777 none CCOC1=CC=CC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 176, 176, 176, 176, 176, 108, 50, 50, 50, 34, 34, 34, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 34, 176, 201, 201, 201, 201, 201, 176, 176, 176, 108, 108, 50, 34, 34, 34, 34, 8, 4, 4, 2, 2, 34, 34, 176] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 589 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113777 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113777 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113777/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113777/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113777 Building REAL300020113778 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113778' /scratch/stefan/7770410/working/building/REAL300020113778 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113778 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113778/0 /scratch/stefan/7770410/working/building/REAL300020113778 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1168) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1168 `/scratch/stefan/7770410/working/3D/1168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CS(C)(=O)=O)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113778.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113778 none CC(CS(C)(=O)=O)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 11, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 26, 59, 74, 106, 106, 106, 26, 26, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 59, 59, 59, 59, 74, 74, 106, 106, 106, 26, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 527 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113778 none CC(CS(C)(=O)=O)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 11, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 89, 156, 183, 201, 201, 201, 89, 89, 43, 43, 43, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 43, 156, 156, 156, 156, 183, 183, 201, 201, 201, 89, 43, 43, 43, 43, 10, 6, 6, 4, 4, 43, 43] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 848 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113778 none CC(CS(C)(=O)=O)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 11, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 19, 30, 30, 30, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 33, 46, 52, 52, 52, 52, 9, 9, 1, 15, 15, 15, 15, 19, 19, 30, 30, 30, 6, 1, 1, 1, 1, 9, 33, 33, 46, 46, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 328 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113778 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113778/1 /scratch/stefan/7770410/working/building/REAL300020113778 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1169) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1169 `/scratch/stefan/7770410/working/3D/1169' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CS(C)(=O)=O)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113778.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113778/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113778 none CC(CS(C)(=O)=O)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 11, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 26, 60, 75, 106, 106, 106, 26, 26, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 60, 60, 60, 60, 75, 75, 106, 106, 106, 26, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 524 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113778 none CC(CS(C)(=O)=O)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 11, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [154, 87, 154, 180, 201, 201, 201, 87, 87, 43, 43, 43, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 43, 154, 154, 154, 154, 180, 180, 201, 201, 201, 87, 43, 43, 43, 43, 10, 6, 6, 4, 4, 43, 43] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 861 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113778 none CC(CS(C)(=O)=O)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 11, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 16, 20, 31, 31, 31, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 32, 45, 51, 51, 51, 51, 9, 9, 1, 16, 16, 16, 16, 20, 20, 31, 31, 31, 6, 1, 1, 1, 1, 9, 32, 32, 45, 45, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 328 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113778 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113778 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113778/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113778/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113778 Building REAL300020113779 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113779' /scratch/stefan/7770410/working/building/REAL300020113779 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113779 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113779/0 /scratch/stefan/7770410/working/building/REAL300020113779 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1170) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1170 `/scratch/stefan/7770410/working/3D/1170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(C)C) `REAL300020113779.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113779 none CCCCC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 80, 38, 38, 38, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 80, 90, 87, 86, 86, 86, 86, 86, 86, 86, 86, 86, 80, 38, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 90, 90, 90, 90, 90, 90, 90] 201 rigid atoms, others: [42, 11, 12, 13, 14, 21, 22, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 453 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113779 none CCCCC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 199, 190, 116, 116, 116, 53, 53, 53, 13, 13, 13, 4, 4, 1, 1, 1, 1, 1, 1, 13, 13, 53, 190, 199, 194, 200, 200, 200, 200, 200, 200, 200, 199, 199, 190, 116, 53, 53, 53, 53, 13, 4, 4, 4, 4, 53, 53, 199, 199, 199, 199, 199, 199, 199] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 802 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113779 none CCCCC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 14, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 32, 46, 50, 50, 50, 50, 11, 11, 1, 14, 21, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 14, 6, 1, 1, 1, 1, 11, 32, 32, 46, 46, 1, 1, 21, 21, 21, 21, 21, 21, 21] 201 rigid atoms, others: [11, 38, 7, 8, 9, 10, 39, 47, 48, 40, 41, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 320 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113779 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113779/1 /scratch/stefan/7770410/working/building/REAL300020113779 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1171) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1171 `/scratch/stefan/7770410/working/3D/1171' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(C)C) `REAL300020113779.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113779/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113779 none CCCCC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 80, 39, 39, 39, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 80, 89, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 80, 39, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 89, 89, 89, 89, 89, 89, 89] 201 rigid atoms, others: [42, 11, 12, 13, 14, 21, 22, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 443 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113779 none CCCCC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 199, 190, 115, 115, 115, 54, 54, 54, 14, 14, 14, 4, 4, 1, 1, 1, 1, 1, 1, 14, 14, 54, 190, 199, 193, 200, 200, 200, 200, 200, 200, 200, 199, 199, 190, 115, 54, 54, 54, 54, 14, 4, 4, 4, 4, 54, 54, 199, 199, 199, 199, 199, 199, 199] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 817 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113779 none CCCCC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 14, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 45, 49, 49, 49, 49, 11, 11, 1, 14, 20, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 14, 6, 1, 1, 1, 1, 11, 31, 31, 45, 45, 1, 1, 20, 20, 20, 20, 20, 20, 20] 201 rigid atoms, others: [11, 38, 7, 8, 9, 10, 39, 47, 48, 40, 41, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 305 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113779 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113779 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113779/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113779/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113779 Building REAL300020113780 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113780' /scratch/stefan/7770410/working/building/REAL300020113780 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113780 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113780/0 /scratch/stefan/7770410/working/building/REAL300020113780 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1172) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1172 `/scratch/stefan/7770410/working/3D/1172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(CC(C)C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113780.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113780 none CC(C)CC(CC(C)C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 85, 39, 85, 85, 85, 85, 39, 39, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 106, 106, 106, 106, 106, 106, 106, 106, 106, 85, 85, 85, 85, 85, 85, 85, 85, 85, 85, 39, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11] 201 rigid atoms, others: [14, 15, 16, 17, 18, 52, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54, 55, 56, 57, 58]) total number of confs: 477 number of broken/clashed sets: 39 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113780 none CC(C)CC(CC(C)C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 106, 201, 201, 201, 201, 106, 106, 49, 49, 49, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 49, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 106, 49, 49, 49, 49, 9, 5, 5, 3, 3, 49, 49] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 760 number of broken/clashed sets: 44 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113780 none CC(C)CC(CC(C)C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 17, 6, 17, 17, 17, 17, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 48, 50, 50, 50, 50, 11, 11, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 11, 33, 33, 48, 48, 1, 1] 201 rigid atoms, others: [11, 12, 13, 14, 15, 48, 49, 50, 51, 57, 58, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 52, 53, 54, 55, 56]) total number of confs: 316 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113780 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113780/1 /scratch/stefan/7770410/working/building/REAL300020113780 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1173) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1173 `/scratch/stefan/7770410/working/3D/1173' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(CC(C)C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113780.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113780/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113780 none CC(C)CC(CC(C)C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 84, 39, 84, 84, 84, 84, 39, 39, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 106, 106, 106, 106, 106, 106, 106, 106, 106, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 39, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11] 201 rigid atoms, others: [14, 15, 16, 17, 18, 52, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54, 55, 56, 57, 58]) total number of confs: 477 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113780 none CC(C)CC(CC(C)C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 106, 201, 201, 201, 201, 106, 106, 50, 50, 50, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 50, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 106, 50, 50, 50, 50, 9, 5, 5, 3, 3, 50, 50] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 760 number of broken/clashed sets: 45 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113780 none CC(C)CC(CC(C)C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 17, 6, 17, 17, 17, 17, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 48, 51, 51, 51, 51, 11, 11, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 11, 33, 33, 48, 48, 1, 1] 201 rigid atoms, others: [11, 12, 13, 14, 15, 48, 49, 50, 51, 57, 58, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 52, 53, 54, 55, 56]) total number of confs: 318 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113780 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113780 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113780/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113780/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113780 Building REAL300020113781 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113781' /scratch/stefan/7770410/working/building/REAL300020113781 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113781 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113781/0 /scratch/stefan/7770410/working/building/REAL300020113781 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1174) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1174 `/scratch/stefan/7770410/working/3D/1174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1) `REAL300020113781.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113781 none CCC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 5, 13, 5, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 28, 42, 42, 42, 42, 42, 10, 10, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 10, 28, 28, 42, 42, 1, 1, 13, 13] 201 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 44, 50, 51, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 244 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113781 none CCC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 20, 69, 20, 69, 69, 20, 20, 20, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 10, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 20, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 69, 69] 201 rigid atoms, others: [45, 14, 13, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 446 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113781 none CCC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 69, 69, 69, 138, 201, 201, 201, 201, 201, 69, 69, 13, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 5, 13, 13, 13, 13, 69, 138, 138, 201, 201, 13, 13, 1, 1] 201 rigid atoms, others: [2, 4, 5, 38, 7, 8, 39, 52, 53, 6, 27, 28] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 837 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113781 none CCC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 62, 201, 62, 201, 201, 62, 62, 62, 43, 43, 43, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 43, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 62, 43, 43, 43, 43, 9, 4, 4, 2, 2, 43, 43, 201, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 1190 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113781 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113781/1 /scratch/stefan/7770410/working/building/REAL300020113781 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1175) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1175 `/scratch/stefan/7770410/working/3D/1175' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1) `REAL300020113781.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113781 none CCC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 5, 13, 5, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 27, 41, 41, 41, 41, 41, 10, 10, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 10, 27, 27, 41, 41, 1, 1, 13, 13] 201 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 44, 50, 51, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 241 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113781 none CCC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 20, 69, 20, 69, 69, 20, 20, 20, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 10, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 20, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 69, 69] 201 rigid atoms, others: [45, 14, 13, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 446 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113781 none CCC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 69, 69, 69, 138, 201, 201, 201, 201, 201, 69, 69, 13, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 5, 13, 13, 13, 13, 69, 138, 138, 201, 201, 13, 13, 1, 1] 201 rigid atoms, others: [2, 4, 5, 38, 7, 8, 39, 52, 53, 6, 27, 28] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 837 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113781 none CCC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 62, 201, 62, 201, 201, 62, 62, 62, 43, 43, 43, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 43, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 62, 43, 43, 43, 43, 9, 4, 4, 2, 2, 43, 43, 201, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 1190 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113781 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113781 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113781/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113781/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113781 Building REAL300020113782 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113782' /scratch/stefan/7770410/working/building/REAL300020113782 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113782 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113782/0 /scratch/stefan/7770410/working/building/REAL300020113782 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1176) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1176 `/scratch/stefan/7770410/working/3D/1176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCC1CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113782.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113782 none O=C(CCCC1CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 20, 21, 25, 42, 42, 42, 42, 1, 1, 1, 1, 1, 7, 7, 7, 19, 29, 29, 29, 29, 29, 7, 7, 1, 20, 20, 25, 25, 25, 25, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 1, 1, 1, 1, 7, 19, 19, 29, 29, 1, 1] 201 rigid atoms, others: [11, 44, 10, 43, 12, 13, 14, 45, 52, 46, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 300 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113782 none O=C(CCCC1CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 80, 74, 89, 130, 130, 130, 130, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 80, 80, 89, 89, 89, 89, 130, 130, 130, 130, 130, 130, 130, 130, 130, 16, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [13, 14, 47, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 616 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113782 none O=C(CCCC1CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 8, 4, 4, 1, 1, 1, 1, 1, 1, 26, 26, 42, 42, 42, 130, 130, 130, 168, 201, 201, 201, 201, 201, 130, 130, 42, 8, 8, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 42, 42, 42, 42, 130, 168, 168, 201, 201, 42, 42] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 39, 40, 41, 36, 38, 37] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 660 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113782 none O=C(CCCC1CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 146, 136, 150, 201, 201, 201, 201, 30, 30, 30, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 30, 146, 146, 150, 150, 150, 150, 201, 201, 201, 201, 201, 201, 201, 201, 201, 42, 30, 30, 30, 30, 7, 4, 4, 2, 2, 30, 30] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 856 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113782 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113782/1 /scratch/stefan/7770410/working/building/REAL300020113782 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1177) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1177 `/scratch/stefan/7770410/working/3D/1177' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCC1CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113782.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113782 none O=C(CCCC1CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 19, 20, 24, 41, 41, 41, 41, 1, 1, 1, 1, 1, 7, 7, 7, 19, 29, 29, 29, 29, 29, 7, 7, 1, 19, 19, 24, 24, 24, 24, 41, 41, 41, 41, 41, 41, 41, 41, 41, 5, 1, 1, 1, 1, 7, 19, 19, 29, 29, 1, 1] 201 rigid atoms, others: [11, 44, 10, 43, 12, 13, 14, 45, 52, 46, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 297 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113782 none O=C(CCCC1CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 79, 74, 89, 130, 130, 130, 130, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 79, 79, 89, 89, 89, 89, 130, 130, 130, 130, 130, 130, 130, 130, 130, 16, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [13, 14, 47, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 619 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113782 none O=C(CCCC1CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 8, 4, 4, 1, 1, 1, 1, 1, 1, 25, 25, 41, 41, 41, 130, 130, 130, 168, 201, 201, 201, 201, 201, 130, 130, 41, 8, 8, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 41, 41, 41, 41, 130, 168, 168, 201, 201, 41, 41] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 39, 40, 41, 36, 38, 37] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 659 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113782 none O=C(CCCC1CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 145, 135, 150, 201, 201, 201, 201, 30, 30, 30, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 30, 145, 145, 150, 150, 150, 150, 201, 201, 201, 201, 201, 201, 201, 201, 201, 41, 30, 30, 30, 30, 7, 4, 4, 2, 2, 30, 30] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 861 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113782 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113782 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113782/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113782/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113782 Building REAL300020113783 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113783' /scratch/stefan/7770410/working/building/REAL300020113783 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113783 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113783/0 /scratch/stefan/7770410/working/building/REAL300020113783 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1178) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1178 `/scratch/stefan/7770410/working/3D/1178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(CC(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1) `REAL300020113783.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113783 none CC1=CC=C(CC(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 26, 15, 6, 15, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 32, 45, 47, 47, 47, 47, 10, 10, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 15, 15, 15, 15, 6, 1, 1, 1, 1, 10, 32, 32, 45, 45, 1, 1, 26, 26] 201 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 44, 50, 51, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 297 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113783 none CC1=CC=C(CC(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 116, 116, 116, 74, 33, 74, 33, 33, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 10, 116, 116, 116, 116, 116, 116, 116, 116, 116, 74, 74, 74, 74, 33, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 116, 116] 201 rigid atoms, others: [45, 14, 13, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 547 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113783 none CC1=CC=C(CC(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 5, 5, 13, 13, 13, 30, 30, 30, 121, 121, 121, 179, 201, 201, 201, 201, 201, 121, 121, 30, 1, 1, 2, 2, 2, 1, 1, 3, 3, 5, 5, 5, 5, 13, 30, 30, 30, 30, 121, 179, 179, 201, 201, 30, 30, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 52, 53, 27, 28, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 666 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113783 none CC1=CC=C(CC(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 174, 101, 174, 101, 101, 46, 46, 46, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 46, 201, 201, 201, 201, 201, 201, 201, 201, 201, 174, 174, 174, 174, 101, 46, 46, 46, 46, 9, 5, 5, 3, 3, 46, 46, 201, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 805 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113783 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113783/1 /scratch/stefan/7770410/working/building/REAL300020113783 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1179) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1179 `/scratch/stefan/7770410/working/3D/1179' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(CC(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1) `REAL300020113783.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113783/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113783 none CC1=CC=C(CC(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 26, 15, 6, 15, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 31, 44, 46, 46, 46, 46, 10, 10, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 15, 15, 15, 15, 6, 1, 1, 1, 1, 10, 31, 31, 44, 44, 1, 1, 26, 26] 201 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 44, 50, 51, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 291 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113783 none CC1=CC=C(CC(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 117, 117, 117, 117, 75, 34, 75, 34, 34, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 10, 117, 117, 117, 117, 117, 117, 117, 117, 117, 75, 75, 75, 75, 34, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 117, 117] 201 rigid atoms, others: [45, 14, 13, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 551 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113783 none CC1=CC=C(CC(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 5, 5, 13, 13, 13, 30, 30, 30, 122, 122, 122, 180, 201, 201, 201, 201, 201, 122, 122, 30, 1, 1, 2, 2, 2, 1, 1, 3, 3, 5, 5, 5, 5, 13, 30, 30, 30, 30, 122, 180, 180, 201, 201, 30, 30, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 52, 53, 27, 28, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 661 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113783 none CC1=CC=C(CC(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 175, 102, 175, 102, 102, 46, 46, 46, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 46, 201, 201, 201, 201, 201, 201, 201, 201, 201, 175, 175, 175, 175, 102, 46, 46, 46, 46, 10, 6, 6, 4, 4, 46, 46, 201, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 804 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113783 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113783 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113783/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113783/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113783 Building REAL300020113784 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113784' /scratch/stefan/7770410/working/building/REAL300020113784 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113784 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113784/0 /scratch/stefan/7770410/working/building/REAL300020113784 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1180) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1180 `/scratch/stefan/7770410/working/3D/1180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C2NC=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C2=C1) `REAL300020113784.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113784 none CC1=CC=C2NC=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 36, 47, 60, 60, 60, 60, 8, 8, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 1, 1, 1, 1, 8, 36, 36, 47, 47, 1, 1, 31] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48]) total number of confs: 245 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113784 none CC1=CC=C2NC=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 91, 91, 91, 91, 28, 28, 28, 8, 8, 8, 1, 1, 1, 1, 1, 9, 14, 19, 19, 19, 19, 1, 1, 8, 91, 91, 91, 91, 91, 91, 91, 91, 91, 28, 8, 8, 8, 8, 1, 9, 9, 14, 14, 8, 8, 91] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 222 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113784 none CC1=CC=C2NC=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 31, 31, 31, 91, 91, 91, 170, 201, 201, 201, 201, 201, 91, 91, 31, 1, 1, 2, 2, 2, 1, 1, 1, 1, 10, 31, 31, 31, 31, 91, 170, 170, 201, 201, 31, 31, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 7, 34, 48, 35, 27, 28, 5] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 726 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113784 none CC1=CC=C2NC=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 131, 131, 131, 69, 69, 69, 27, 27, 27, 8, 4, 1, 1, 1, 1, 1, 1, 27, 27, 69, 201, 201, 201, 201, 201, 201, 201, 201, 201, 131, 69, 69, 69, 69, 27, 8, 8, 4, 4, 69, 69, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 476 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113784 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113784/1 /scratch/stefan/7770410/working/building/REAL300020113784 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1181) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1181 `/scratch/stefan/7770410/working/3D/1181' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C2NC=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C2=C1) `REAL300020113784.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113784 none CC1=CC=C2NC=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 36, 47, 60, 60, 60, 60, 8, 8, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 1, 1, 1, 1, 8, 36, 36, 47, 47, 1, 1, 31] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48]) total number of confs: 245 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113784 none CC1=CC=C2NC=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 90, 90, 90, 90, 28, 28, 28, 8, 8, 8, 1, 1, 1, 1, 1, 9, 14, 19, 19, 19, 19, 1, 1, 8, 90, 90, 90, 90, 90, 90, 90, 90, 90, 28, 8, 8, 8, 8, 1, 9, 9, 14, 14, 8, 8, 90] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 221 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113784 none CC1=CC=C2NC=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 31, 31, 31, 90, 90, 90, 169, 201, 201, 201, 201, 201, 90, 90, 31, 1, 1, 2, 2, 2, 1, 1, 1, 1, 10, 31, 31, 31, 31, 90, 169, 169, 201, 201, 31, 31, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 7, 34, 48, 35, 27, 28, 5] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 730 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113784 none CC1=CC=C2NC=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 131, 131, 131, 69, 69, 69, 27, 27, 27, 8, 4, 1, 1, 1, 1, 1, 1, 27, 27, 69, 201, 201, 201, 201, 201, 201, 201, 201, 201, 131, 69, 69, 69, 69, 27, 8, 8, 4, 4, 69, 69, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 474 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113784 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113784 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113784/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113784/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113784 Building REAL300020113785 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113785' /scratch/stefan/7770410/working/building/REAL300020113785 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113785 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113785/0 /scratch/stefan/7770410/working/building/REAL300020113785 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1182) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1182 `/scratch/stefan/7770410/working/3D/1182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N(C)C1=O) `REAL300020113785.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113785 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 5, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 8, 11, 11, 11, 11, 11, 5, 5, 1, 13, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 5, 8, 8, 11, 11, 1, 1, 13, 13, 13] 22 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 65 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113785 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 5, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 10, 10, 10, 5, 5, 5, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17, 10, 5, 5, 5, 5, 1, 5, 5, 7, 7, 5, 5, 17, 17, 17] 22 rigid atoms, others: [36, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 65 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113785 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 5, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 8, 13, 13, 13, 17, 17, 17, 20, 22, 22, 22, 22, 22, 17, 17, 13, 1, 1, 1, 1, 2, 2, 2, 1, 8, 13, 13, 13, 13, 17, 20, 20, 22, 22, 13, 13, 2, 2, 2] 22 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113785 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 5, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 16, 16, 16, 11, 11, 11, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 11, 22, 22, 22, 22, 22, 22, 22, 22, 16, 11, 11, 11, 11, 7, 4, 4, 2, 2, 11, 11, 22, 22, 22] 22 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 62 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113785 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113785/1 /scratch/stefan/7770410/working/building/REAL300020113785 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1183) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1183 `/scratch/stefan/7770410/working/3D/1183' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N(C)C1=O) `REAL300020113785.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113785/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113785 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 5, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 8, 11, 11, 11, 11, 11, 5, 5, 1, 13, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 5, 8, 8, 11, 11, 1, 1, 13, 13, 13] 22 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 65 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113785 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 5, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 10, 10, 10, 5, 5, 5, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17, 10, 5, 5, 5, 5, 1, 5, 5, 7, 7, 5, 5, 17, 17, 17] 22 rigid atoms, others: [36, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 65 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113785 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 5, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 8, 13, 13, 13, 17, 17, 17, 20, 22, 22, 22, 22, 22, 17, 17, 13, 1, 1, 1, 1, 2, 2, 2, 1, 8, 13, 13, 13, 13, 17, 20, 20, 22, 22, 13, 13, 2, 2, 2] 22 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113785 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 5, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 16, 16, 16, 11, 11, 11, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 11, 22, 22, 22, 22, 22, 22, 22, 22, 16, 11, 11, 11, 11, 7, 4, 4, 2, 2, 11, 11, 22, 22, 22] 22 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 62 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113785 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113785 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113785/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113785/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113785 Building REAL300020113786 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113786' /scratch/stefan/7770410/working/building/REAL300020113786 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113786 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113786/0 /scratch/stefan/7770410/working/building/REAL300020113786 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1184) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1184 `/scratch/stefan/7770410/working/3D/1184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NSC(C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113786.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113786 none CC1=NSC(C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 16, 18, 18, 18, 18, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 28, 41, 42, 42, 42, 42, 11, 11, 1, 18, 18, 18, 18, 18, 18, 5, 1, 1, 1, 1, 11, 28, 28, 41, 41, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 200 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113786 none CC1=NSC(C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 79, 88, 88, 88, 88, 26, 26, 26, 11, 11, 11, 1, 1, 1, 1, 1, 5, 7, 8, 8, 8, 8, 1, 1, 11, 88, 88, 88, 88, 88, 88, 26, 11, 11, 11, 11, 1, 5, 5, 7, 7, 11, 11] 201 rigid atoms, others: [37, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 207 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113786 none CC1=NSC(C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 18, 18, 18, 88, 88, 88, 156, 201, 201, 201, 201, 201, 88, 88, 18, 2, 2, 2, 2, 2, 2, 7, 18, 18, 18, 18, 88, 156, 156, 201, 201, 18, 18] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 773 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113786 none CC1=NSC(C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 192, 201, 201, 201, 201, 75, 75, 75, 42, 42, 42, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 42, 201, 201, 201, 201, 201, 201, 75, 42, 42, 42, 42, 9, 5, 5, 3, 3, 42, 42] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 426 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113786 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113786/1 /scratch/stefan/7770410/working/building/REAL300020113786 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1185) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1185 `/scratch/stefan/7770410/working/3D/1185' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NSC(C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113786.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113786 none CC1=NSC(C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 16, 18, 18, 18, 18, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 28, 41, 42, 42, 42, 42, 11, 11, 1, 18, 18, 18, 18, 18, 18, 5, 1, 1, 1, 1, 11, 28, 28, 41, 41, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 200 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113786 none CC1=NSC(C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 79, 88, 88, 88, 88, 26, 26, 26, 11, 11, 11, 1, 1, 1, 1, 1, 5, 7, 8, 8, 8, 8, 1, 1, 11, 88, 88, 88, 88, 88, 88, 26, 11, 11, 11, 11, 1, 5, 5, 7, 7, 11, 11] 201 rigid atoms, others: [37, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 207 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113786 none CC1=NSC(C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 18, 18, 18, 88, 88, 88, 156, 201, 201, 201, 201, 201, 88, 88, 18, 2, 2, 2, 2, 2, 2, 7, 18, 18, 18, 18, 88, 156, 156, 201, 201, 18, 18] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 773 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113786 none CC1=NSC(C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 192, 201, 201, 201, 201, 75, 75, 75, 42, 42, 42, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 42, 201, 201, 201, 201, 201, 201, 75, 42, 42, 42, 42, 9, 5, 5, 3, 3, 42, 42] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 426 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113786 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113786 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113786/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113786/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113786 Building REAL300020113787 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113787' /scratch/stefan/7770410/working/building/REAL300020113787 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113787 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113787/0 /scratch/stefan/7770410/working/building/REAL300020113787 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1186) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1186 `/scratch/stefan/7770410/working/3D/1186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC(C2CC2)=C1) `REAL300020113787.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113787 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 8, 18, 58, 58, 33, 58, 58, 94, 94, 58, 18, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 58, 58, 33, 94, 94, 94, 94, 94, 58] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 358 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113787 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 3, 9, 9, 21, 21, 21, 94, 94, 94, 162, 201, 201, 201, 201, 201, 94, 94, 21, 3, 3, 3, 3, 1, 1, 1, 1, 3, 9, 21, 21, 21, 21, 94, 162, 162, 201, 201, 21, 21, 3, 3, 3, 1, 1, 1, 1, 1, 3] 201 rigid atoms, others: [43, 44, 45, 46, 47, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48]) total number of confs: 745 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113787 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 42, 42, 42, 14, 14, 14, 6, 3, 1, 1, 1, 1, 1, 1, 14, 14, 42, 61, 180, 180, 104, 180, 180, 201, 201, 180, 61, 42, 42, 42, 42, 14, 6, 6, 3, 3, 42, 42, 180, 180, 104, 201, 201, 201, 201, 201, 180] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 646 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113787 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 24, 36, 38, 38, 38, 38, 8, 8, 1, 5, 12, 12, 8, 12, 12, 21, 21, 12, 5, 1, 1, 1, 1, 8, 24, 24, 36, 36, 1, 1, 12, 12, 8, 21, 21, 21, 21, 21, 12] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 219 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113787 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 12, 12, 12, 58, 58, 58, 124, 178, 180, 180, 180, 180, 58, 58, 12, 1, 1, 1, 1, 1, 1, 3, 3, 1, 5, 12, 12, 12, 12, 58, 124, 124, 178, 178, 12, 12, 1, 1, 1, 3, 3, 3, 3, 3, 1] 201 rigid atoms, others: [1, 40, 41, 42, 48, 19, 20, 21, 22, 23, 24, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47]) total number of confs: 744 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113787 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113787/1 /scratch/stefan/7770410/working/building/REAL300020113787 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1187) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1187 `/scratch/stefan/7770410/working/3D/1187' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC(C2CC2)=C1) `REAL300020113787.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113787 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 8, 18, 58, 58, 33, 58, 58, 94, 94, 58, 18, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 58, 58, 33, 94, 94, 94, 94, 94, 58] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 358 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113787 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 3, 9, 9, 21, 21, 21, 94, 94, 94, 162, 201, 201, 201, 201, 201, 94, 94, 21, 3, 3, 3, 3, 1, 1, 1, 1, 3, 9, 21, 21, 21, 21, 94, 162, 162, 201, 201, 21, 21, 3, 3, 3, 1, 1, 1, 1, 1, 3] 201 rigid atoms, others: [43, 44, 45, 46, 47, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48]) total number of confs: 742 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113787 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 41, 41, 41, 13, 13, 13, 7, 4, 1, 1, 1, 1, 1, 1, 13, 13, 41, 61, 180, 180, 105, 180, 180, 201, 201, 180, 61, 41, 41, 41, 41, 13, 7, 7, 4, 4, 41, 41, 180, 180, 105, 201, 201, 201, 201, 201, 180] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 647 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113787 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 24, 36, 38, 38, 38, 38, 8, 8, 1, 5, 12, 12, 8, 12, 12, 21, 21, 12, 5, 1, 1, 1, 1, 8, 24, 24, 36, 36, 1, 1, 12, 12, 8, 21, 21, 21, 21, 21, 12] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 219 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113787 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 12, 12, 12, 58, 58, 58, 123, 177, 179, 179, 179, 179, 58, 58, 12, 1, 1, 1, 1, 1, 1, 3, 3, 1, 5, 12, 12, 12, 12, 58, 123, 123, 177, 177, 12, 12, 1, 1, 1, 3, 3, 3, 3, 3, 1] 201 rigid atoms, others: [1, 40, 41, 42, 48, 19, 20, 21, 22, 23, 24, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47]) total number of confs: 741 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113787 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113787 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113787/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113787/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113787 Building REAL300020113788 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113788' /scratch/stefan/7770410/working/building/REAL300020113788 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113788 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113788/0 /scratch/stefan/7770410/working/building/REAL300020113788 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1188) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1188 `/scratch/stefan/7770410/working/3D/1188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CN=C2NC=CC=C12)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113788.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113788 none O=C(CC1=CN=C2NC=CC=C12)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 21, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 7, 7, 7, 21, 33, 33, 33, 33, 33, 7, 7, 1, 21, 21, 43, 43, 43, 43, 43, 6, 1, 1, 1, 1, 7, 21, 21, 33, 33, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 46, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 247 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113788 none O=C(CC1=CN=C2NC=CC=C12)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 76, 124, 124, 124, 124, 124, 124, 124, 124, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 76, 76, 124, 124, 124, 124, 124, 22, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 373 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113788 none O=C(CC1=CN=C2NC=CC=C12)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 43, 43, 43, 124, 124, 124, 170, 201, 201, 201, 201, 201, 124, 124, 43, 8, 8, 1, 1, 1, 1, 1, 27, 43, 43, 43, 43, 124, 170, 170, 201, 201, 43, 43] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 678 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113788 none O=C(CC1=CN=C2NC=CC=C12)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 157, 201, 201, 201, 201, 201, 201, 201, 201, 34, 34, 34, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 34, 157, 157, 201, 201, 201, 201, 201, 65, 34, 34, 34, 34, 8, 4, 4, 2, 2, 34, 34] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 668 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113788 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113788/1 /scratch/stefan/7770410/working/building/REAL300020113788 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1189) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1189 `/scratch/stefan/7770410/working/3D/1189' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CN=C2NC=CC=C12)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113788.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113788 none O=C(CC1=CN=C2NC=CC=C12)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 21, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 7, 7, 7, 21, 33, 33, 33, 33, 33, 7, 7, 1, 21, 21, 43, 43, 43, 43, 43, 6, 1, 1, 1, 1, 7, 21, 21, 33, 33, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 46, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 247 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113788 none O=C(CC1=CN=C2NC=CC=C12)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 76, 125, 125, 125, 125, 125, 125, 125, 125, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 76, 76, 125, 125, 125, 125, 125, 22, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 375 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113788 none O=C(CC1=CN=C2NC=CC=C12)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 43, 43, 43, 125, 125, 125, 170, 201, 201, 201, 201, 201, 125, 125, 43, 8, 8, 1, 1, 1, 1, 1, 27, 43, 43, 43, 43, 125, 170, 170, 201, 201, 43, 43] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 675 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113788 none O=C(CC1=CN=C2NC=CC=C12)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 156, 201, 201, 201, 201, 201, 201, 201, 201, 33, 33, 33, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 33, 156, 156, 201, 201, 201, 201, 201, 64, 33, 33, 33, 33, 7, 4, 4, 2, 2, 33, 33] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 668 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113788 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113788 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113788/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113788/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113788 Building REAL300020113789 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113789' /scratch/stefan/7770410/working/building/REAL300020113789 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113789 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113789/0 /scratch/stefan/7770410/working/building/REAL300020113789 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1190) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1190 `/scratch/stefan/7770410/working/3D/1190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(C)(CC)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113789.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113789 none CCCCCC(C)(CC)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 94, 94, 60, 39, 60, 60, 71, 39, 39, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 101, 101, 101, 101, 101, 101, 101, 94, 94, 94, 94, 60, 60, 60, 71, 71, 71, 71, 71, 39, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11] 201 rigid atoms, others: [14, 15, 16, 17, 18, 52, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54, 55, 56, 57, 58]) total number of confs: 518 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113789 none CCCCCC(C)(CC)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 194, 194, 159, 119, 159, 159, 176, 119, 119, 56, 56, 56, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 56, 201, 201, 201, 201, 201, 201, 201, 194, 194, 194, 194, 159, 159, 159, 176, 176, 176, 176, 176, 119, 56, 56, 56, 56, 11, 6, 6, 4, 4, 56, 56] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 865 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113789 none CCCCCC(C)(CC)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 21, 21, 12, 6, 12, 12, 14, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 36, 49, 56, 56, 56, 56, 11, 11, 1, 25, 25, 25, 25, 25, 25, 25, 21, 21, 21, 21, 12, 12, 12, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 11, 36, 36, 49, 49, 1, 1] 201 rigid atoms, others: [11, 12, 13, 14, 15, 48, 49, 50, 51, 57, 58, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 52, 53, 54, 55, 56]) total number of confs: 320 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113789 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113789/1 /scratch/stefan/7770410/working/building/REAL300020113789 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1191) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1191 `/scratch/stefan/7770410/working/3D/1191' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(C)(CC)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113789.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113789 none CCCCCC(C)(CC)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 96, 96, 62, 40, 62, 62, 73, 40, 40, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 103, 103, 103, 103, 103, 103, 103, 96, 96, 96, 96, 62, 62, 62, 73, 73, 73, 73, 73, 40, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11] 201 rigid atoms, others: [14, 15, 16, 17, 18, 52, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54, 55, 56, 57, 58]) total number of confs: 523 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113789 none CCCCCC(C)(CC)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 194, 194, 159, 118, 159, 159, 176, 118, 118, 56, 56, 56, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 56, 201, 201, 201, 201, 201, 201, 201, 194, 194, 194, 194, 159, 159, 159, 176, 176, 176, 176, 176, 118, 56, 56, 56, 56, 11, 6, 6, 4, 4, 56, 56] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 864 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113789 none CCCCCC(C)(CC)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 21, 21, 12, 6, 12, 12, 14, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 36, 49, 56, 56, 56, 56, 11, 11, 1, 25, 25, 25, 25, 25, 25, 25, 21, 21, 21, 21, 12, 12, 12, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 11, 36, 36, 49, 49, 1, 1] 201 rigid atoms, others: [11, 12, 13, 14, 15, 48, 49, 50, 51, 57, 58, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 52, 53, 54, 55, 56]) total number of confs: 320 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113789 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113789 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113789/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113789/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113789 Building REAL300020113790 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113790' /scratch/stefan/7770410/working/building/REAL300020113790 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113790 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113790/0 /scratch/stefan/7770410/working/building/REAL300020113790 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1192) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1192 `/scratch/stefan/7770410/working/3D/1192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C2=C1CCC2) `REAL300020113790.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113790 none CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C2=C1CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 28, 31, 31, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 35, 45, 45, 45, 45, 45, 13, 13, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 1, 1, 1, 1, 13, 35, 35, 45, 45, 1, 1, 31, 31, 31, 31, 31, 31] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 44, 45, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51]) total number of confs: 227 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113790 none CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C2=C1CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [143, 141, 143, 143, 54, 54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 143, 143, 143, 143, 143, 143, 143, 143, 143, 143, 54, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 143, 143, 143, 143, 143, 143] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 305 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113790 none CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C2=C1CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 31, 31, 31, 143, 143, 143, 182, 201, 201, 201, 201, 201, 143, 143, 31, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 10, 31, 31, 31, 31, 143, 182, 182, 201, 201, 31, 31, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 46, 47, 48, 49, 50, 51, 24, 25, 26, 27, 28, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 546 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113790 none CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C2=C1CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 106, 106, 106, 45, 45, 45, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 45, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 106, 45, 45, 45, 45, 8, 4, 4, 2, 2, 45, 45, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 439 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113790 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113790/1 /scratch/stefan/7770410/working/building/REAL300020113790 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1193) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1193 `/scratch/stefan/7770410/working/3D/1193' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C2=C1CCC2) `REAL300020113790.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113790 none CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C2=C1CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 28, 31, 31, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 35, 45, 45, 45, 45, 45, 13, 13, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 1, 1, 1, 1, 13, 35, 35, 45, 45, 1, 1, 31, 31, 31, 31, 31, 31] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 44, 45, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51]) total number of confs: 227 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113790 none CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C2=C1CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [143, 141, 143, 143, 54, 54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 143, 143, 143, 143, 143, 143, 143, 143, 143, 143, 54, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 143, 143, 143, 143, 143, 143] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 305 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113790 none CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C2=C1CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 31, 31, 31, 143, 143, 143, 182, 201, 201, 201, 201, 201, 143, 143, 31, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 10, 31, 31, 31, 31, 143, 182, 182, 201, 201, 31, 31, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 46, 47, 48, 49, 50, 51, 24, 25, 26, 27, 28, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 546 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113790 none CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C2=C1CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 106, 106, 106, 45, 45, 45, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 45, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 106, 45, 45, 45, 45, 8, 4, 4, 2, 2, 45, 45, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 439 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113790 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113790 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113790/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113790/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113790 Building REAL300020113791 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113791' /scratch/stefan/7770410/working/building/REAL300020113791 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113791 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113791/0 /scratch/stefan/7770410/working/building/REAL300020113791 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1194) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1194 `/scratch/stefan/7770410/working/3D/1194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C)CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1) `REAL300020113791.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113791 none CC1CC(C)CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 28, 28, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 47, 49, 49, 49, 49, 11, 11, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 1, 1, 1, 1, 11, 33, 33, 47, 47, 1, 1, 28, 28] 201 rigid atoms, others: [43, 9, 10, 11, 12, 13, 44, 50, 51, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 259 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113791 none CC1CC(C)CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 95, 95, 95, 33, 33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 33, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 95, 95] 201 rigid atoms, others: [12, 45, 14, 13, 16, 23, 24, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 293 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113791 none CC1CC(C)CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 28, 28, 28, 95, 95, 95, 178, 201, 201, 201, 201, 201, 95, 95, 28, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 8, 28, 28, 28, 28, 95, 178, 178, 201, 201, 28, 28, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 38, 7, 33, 37, 52, 53, 39, 26, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 675 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113791 none CC1CC(C)CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 108, 108, 108, 49, 49, 49, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 49, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 108, 49, 49, 49, 49, 10, 6, 6, 4, 4, 49, 49, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 589 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113791 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113791/1 /scratch/stefan/7770410/working/building/REAL300020113791 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1195) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1195 `/scratch/stefan/7770410/working/3D/1195' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C)CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1) `REAL300020113791.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113791 none CC1CC(C)CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 28, 28, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 47, 49, 49, 49, 49, 11, 11, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 1, 1, 1, 1, 11, 33, 33, 47, 47, 1, 1, 28, 28] 201 rigid atoms, others: [43, 9, 10, 11, 12, 13, 44, 50, 51, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 259 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113791 none CC1CC(C)CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 96, 96, 96, 33, 33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 33, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 96, 96] 201 rigid atoms, others: [12, 45, 14, 13, 16, 23, 24, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 295 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113791 none CC1CC(C)CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 28, 28, 28, 96, 96, 96, 178, 201, 201, 201, 201, 201, 96, 96, 28, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 8, 28, 28, 28, 28, 96, 178, 178, 201, 201, 28, 28, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 38, 7, 33, 37, 52, 53, 39, 26, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 670 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113791 none CC1CC(C)CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 107, 107, 107, 50, 50, 50, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 50, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 107, 50, 50, 50, 50, 11, 6, 6, 4, 4, 50, 50, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 585 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113791 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113791 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113791/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113791/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113791 Building REAL300020113792 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113792' /scratch/stefan/7770410/working/building/REAL300020113792 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113792 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113792/0 /scratch/stefan/7770410/working/building/REAL300020113792 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1196) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1196 `/scratch/stefan/7770410/working/3D/1196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(F)C=C1) `REAL300020113792.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113792 none CCC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 82, 39, 39, 39, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 11, 11, 11, 11, 1, 1, 11, 82, 84, 84, 82, 84, 84, 84, 90, 90, 90, 90, 90, 82, 39, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 84, 84, 84, 84] 201 rigid atoms, others: [8, 9, 10, 11, 12, 40, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 380 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113792 none CCC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 198, 122, 122, 122, 57, 57, 57, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 57, 198, 201, 201, 198, 201, 201, 201, 201, 201, 201, 201, 201, 198, 122, 57, 57, 57, 57, 13, 6, 6, 4, 4, 57, 57, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 709 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113792 none CCC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 16, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 47, 55, 55, 55, 55, 11, 11, 1, 16, 17, 17, 16, 17, 17, 17, 19, 19, 19, 19, 19, 16, 6, 1, 1, 1, 1, 11, 33, 33, 47, 47, 1, 1, 17, 17, 17, 17] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 39, 45, 46, 21, 38, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50]) total number of confs: 284 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113792 none CCC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 3, 1, 3, 7, 7, 7, 17, 17, 17, 84, 84, 84, 148, 199, 201, 201, 201, 201, 84, 84, 17, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 3, 7, 17, 17, 17, 17, 84, 148, 148, 199, 199, 17, 17, 1, 1, 1, 1] 201 rigid atoms, others: [2, 47, 48, 49, 50, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 777 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113792 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113792/1 /scratch/stefan/7770410/working/building/REAL300020113792 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1197) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1197 `/scratch/stefan/7770410/working/3D/1197' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(F)C=C1) `REAL300020113792.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113792 none CCC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 82, 39, 39, 39, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 12, 12, 12, 12, 1, 1, 11, 82, 84, 84, 82, 84, 84, 84, 90, 90, 90, 90, 90, 82, 39, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 84, 84, 84, 84] 201 rigid atoms, others: [8, 9, 10, 11, 12, 40, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 383 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113792 none CCC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 198, 121, 121, 121, 56, 56, 56, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 56, 198, 201, 201, 198, 201, 201, 201, 201, 201, 201, 201, 201, 198, 121, 56, 56, 56, 56, 13, 6, 6, 4, 4, 56, 56, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 713 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113792 none CCC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 16, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 35, 49, 57, 57, 57, 57, 11, 11, 1, 16, 17, 17, 16, 17, 17, 17, 19, 19, 19, 19, 19, 16, 6, 1, 1, 1, 1, 11, 35, 35, 49, 49, 1, 1, 17, 17, 17, 17] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 39, 45, 46, 21, 38, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113792 none CCC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 3, 1, 3, 7, 7, 7, 17, 17, 17, 84, 84, 84, 148, 199, 201, 201, 201, 201, 84, 84, 17, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 3, 7, 17, 17, 17, 17, 84, 148, 148, 199, 199, 17, 17, 1, 1, 1, 1] 201 rigid atoms, others: [2, 47, 48, 49, 50, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 771 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113792 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113792 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113792/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113792/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113792 Building REAL300020113793 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113793' /scratch/stefan/7770410/working/building/REAL300020113793 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113793 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113793/0 /scratch/stefan/7770410/working/building/REAL300020113793 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1198) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1198 `/scratch/stefan/7770410/working/3D/1198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113793.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113793 none CC(=O)N1CCC[C@@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 21, 38, 21, 21, 21, 21, 6, 21, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 46, 63, 75, 75, 75, 75, 13, 13, 1, 38, 38, 38, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 13, 46, 46, 63, 63, 1, 1] 201 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 375 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113793 none CC(=O)N1CCC[C@@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [126, 92, 126, 92, 92, 92, 92, 49, 92, 49, 49, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 13, 126, 126, 126, 92, 92, 92, 92, 92, 92, 49, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 430 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113793 none CC(=O)N1CCC[C@@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 21, 21, 92, 92, 92, 151, 180, 180, 180, 180, 180, 92, 92, 21, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 21, 92, 151, 151, 180, 180, 21, 21] 201 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 9, 35, 36, 33, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 606 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113793 none CC(=O)N1CCC[C@@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 181, 201, 181, 181, 181, 181, 138, 181, 138, 138, 72, 72, 72, 14, 14, 14, 7, 4, 1, 1, 1, 1, 1, 1, 14, 14, 72, 201, 201, 201, 181, 181, 181, 181, 181, 181, 138, 72, 72, 72, 72, 14, 7, 7, 4, 4, 72, 72] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 618 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113793 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113793/1 /scratch/stefan/7770410/working/building/REAL300020113793 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1199) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1199 `/scratch/stefan/7770410/working/3D/1199' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113793.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113793 none CC(=O)N1CCC[C@@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 21, 38, 21, 21, 21, 21, 6, 21, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 46, 63, 75, 75, 75, 75, 13, 13, 1, 38, 38, 38, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 13, 46, 46, 63, 63, 1, 1] 201 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 375 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113793 none CC(=O)N1CCC[C@@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 91, 124, 91, 91, 91, 91, 49, 91, 49, 49, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 13, 124, 124, 124, 91, 91, 91, 91, 91, 91, 49, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 424 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113793 none CC(=O)N1CCC[C@@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 21, 21, 91, 91, 91, 152, 181, 181, 181, 181, 181, 91, 91, 21, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 21, 91, 152, 152, 181, 181, 21, 21] 201 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 9, 35, 36, 33, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 617 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113793 none CC(=O)N1CCC[C@@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 180, 201, 180, 180, 180, 180, 133, 180, 133, 133, 67, 67, 67, 13, 13, 13, 7, 5, 1, 1, 1, 1, 1, 1, 13, 13, 67, 201, 201, 201, 180, 180, 180, 180, 180, 180, 133, 67, 67, 67, 67, 13, 7, 7, 4, 4, 67, 67] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 615 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113793 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113793 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113793/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113793/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113793 Building REAL300020113794 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113794' /scratch/stefan/7770410/working/building/REAL300020113794 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113794 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113794/0 /scratch/stefan/7770410/working/building/REAL300020113794 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1200) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1200 `/scratch/stefan/7770410/working/3D/1200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1) `REAL300020113794.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113794 none CC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 13, 19, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 48, 66, 83, 83, 83, 83, 11, 11, 1, 13, 19, 19, 19, 19, 19, 19, 19, 13, 13, 6, 1, 1, 1, 1, 11, 48, 48, 66, 66, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 354 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113794 none CC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 68, 101, 68, 68, 68, 41, 41, 41, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 11, 68, 101, 101, 101, 101, 101, 101, 101, 68, 68, 41, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 395 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113794 none CC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 68, 68, 68, 143, 187, 201, 201, 201, 201, 68, 68, 13, 1, 3, 3, 3, 2, 2, 2, 2, 1, 1, 4, 13, 13, 13, 13, 68, 143, 143, 187, 187, 13, 13] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 741 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113794 none CC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 186, 186, 186, 84, 84, 84, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 84, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 186, 84, 84, 84, 84, 17, 6, 6, 4, 4, 84, 84] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 549 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113794 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113794/1 /scratch/stefan/7770410/working/building/REAL300020113794 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1201) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1201 `/scratch/stefan/7770410/working/3D/1201' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1) `REAL300020113794.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113794/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113794 none CC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 12, 19, 12, 12, 12, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 47, 65, 81, 81, 81, 81, 11, 11, 1, 12, 19, 19, 19, 19, 19, 19, 19, 12, 12, 6, 1, 1, 1, 1, 11, 47, 47, 65, 65, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 354 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113794 none CC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 67, 99, 67, 67, 67, 41, 41, 41, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 17, 17, 17, 17, 1, 1, 11, 67, 99, 99, 99, 99, 99, 99, 99, 67, 67, 41, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 390 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113794 none CC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 67, 67, 67, 143, 187, 201, 201, 201, 201, 67, 67, 12, 1, 3, 3, 3, 2, 2, 2, 2, 1, 1, 4, 12, 12, 12, 12, 67, 143, 143, 187, 187, 12, 12] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 742 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113794 none CC(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 187, 187, 187, 82, 82, 82, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 82, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 187, 82, 82, 82, 82, 18, 6, 6, 4, 4, 82, 82] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 556 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113794 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113794 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113794/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113794/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113794 Building REAL300020113795 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113795' /scratch/stefan/7770410/working/building/REAL300020113795 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113795 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113795/0 /scratch/stefan/7770410/working/building/REAL300020113795 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1202) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1202 `/scratch/stefan/7770410/working/3D/1202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1) `REAL300020113795.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113795 none CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 9, 14, 9, 9, 9, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 48, 67, 81, 81, 81, 81, 12, 12, 1, 9, 9, 14, 14, 14, 14, 14, 14, 9, 9, 6, 1, 1, 1, 1, 12, 48, 48, 67, 67, 1, 1, 9] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48]) total number of confs: 331 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113795 none CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 64, 98, 64, 64, 64, 49, 49, 49, 12, 12, 12, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 12, 64, 64, 98, 98, 98, 98, 98, 98, 64, 64, 49, 12, 12, 12, 12, 1, 8, 8, 10, 10, 12, 12, 64] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 325 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113795 none CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 64, 64, 64, 146, 188, 201, 201, 201, 201, 64, 64, 9, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 3, 9, 9, 9, 9, 64, 146, 146, 188, 188, 9, 9, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 48, 35, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 733 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113795 none CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 197, 197, 197, 81, 81, 81, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 81, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 197, 81, 81, 81, 81, 13, 6, 6, 4, 4, 81, 81, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 548 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113795 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113795/1 /scratch/stefan/7770410/working/building/REAL300020113795 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1203) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1203 `/scratch/stefan/7770410/working/3D/1203' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1) `REAL300020113795.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113795 none CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 9, 14, 9, 9, 9, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 49, 67, 81, 81, 81, 81, 12, 12, 1, 9, 9, 14, 14, 14, 14, 14, 14, 9, 9, 6, 1, 1, 1, 1, 12, 49, 49, 67, 67, 1, 1, 9] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48]) total number of confs: 328 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113795 none CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 64, 99, 64, 64, 64, 49, 49, 49, 12, 12, 12, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 12, 64, 64, 99, 99, 99, 99, 99, 99, 64, 64, 49, 12, 12, 12, 12, 1, 8, 8, 10, 10, 12, 12, 64] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 331 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113795 none CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 64, 64, 64, 148, 189, 201, 201, 201, 201, 64, 64, 9, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 3, 9, 9, 9, 9, 64, 148, 148, 189, 189, 9, 9, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 48, 35, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 734 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113795 none CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 197, 197, 197, 81, 81, 81, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 81, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 197, 81, 81, 81, 81, 13, 6, 6, 4, 4, 81, 81, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 548 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113795 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113795 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113795/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113795/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113795 Building REAL300020113796 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113796' /scratch/stefan/7770410/working/building/REAL300020113796 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113796 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113796/0 /scratch/stefan/7770410/working/building/REAL300020113796 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1204) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1204 `/scratch/stefan/7770410/working/3D/1204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1) `REAL300020113796.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113796 none CC1(C)CCCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 31, 44, 47, 47, 47, 47, 10, 10, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 10, 31, 31, 44, 44, 1, 1, 18, 18] 201 rigid atoms, others: [43, 9, 10, 11, 12, 13, 44, 50, 51, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 223 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113796 none CC1(C)CCCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 93, 93, 93, 31, 31, 31, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 10, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 31, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 93, 93] 201 rigid atoms, others: [12, 45, 14, 13, 16, 23, 24, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 269 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113796 none CC1(C)CCCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 93, 93, 93, 158, 201, 201, 201, 201, 201, 93, 93, 18, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 18, 18, 18, 18, 93, 158, 158, 201, 201, 18, 18, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 34, 35, 52, 53, 39, 36, 26, 38, 5, 37, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 741 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113796 none CC1(C)CCCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 90, 90, 90, 48, 48, 48, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 48, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 90, 48, 48, 48, 48, 10, 6, 6, 4, 4, 48, 48, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 579 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113796 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113796/1 /scratch/stefan/7770410/working/building/REAL300020113796 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1205) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1205 `/scratch/stefan/7770410/working/3D/1205' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1) `REAL300020113796.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113796 none CC1(C)CCCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 30, 43, 46, 46, 46, 46, 10, 10, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 10, 30, 30, 43, 43, 1, 1, 18, 18] 201 rigid atoms, others: [43, 9, 10, 11, 12, 13, 44, 50, 51, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 220 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113796 none CC1(C)CCCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 94, 94, 94, 31, 31, 31, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 10, 94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 31, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 94, 94] 201 rigid atoms, others: [12, 45, 14, 13, 16, 23, 24, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 273 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113796 none CC1(C)CCCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 94, 94, 94, 158, 201, 201, 201, 201, 201, 94, 94, 18, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 18, 18, 18, 18, 94, 158, 158, 201, 201, 18, 18, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 34, 35, 52, 53, 39, 36, 26, 38, 5, 37, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 736 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113796 none CC1(C)CCCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 89, 89, 89, 47, 47, 47, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 47, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 89, 47, 47, 47, 47, 10, 5, 5, 3, 3, 47, 47, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 580 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113796 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113796 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113796/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113796/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113796 Building REAL300020113797 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113797' /scratch/stefan/7770410/working/building/REAL300020113797 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113797 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113797/0 /scratch/stefan/7770410/working/building/REAL300020113797 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1206) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1206 `/scratch/stefan/7770410/working/3D/1206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1CC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113797.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113797 none CC1=CC=CC=C1CC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 25, 33, 33, 25, 15, 6, 15, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 28, 41, 42, 42, 42, 42, 9, 9, 1, 33, 33, 33, 33, 25, 33, 33, 25, 25, 15, 15, 15, 15, 6, 1, 1, 1, 1, 9, 28, 28, 41, 41, 1, 1] 201 rigid atoms, others: [45, 44, 43, 12, 13, 14, 15, 16, 52, 46, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 310 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113797 none CC1=CC=CC=C1CC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 119, 97, 119, 119, 97, 64, 29, 64, 29, 29, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 9, 119, 119, 119, 119, 97, 119, 119, 97, 97, 64, 64, 64, 64, 29, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [15, 47, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 557 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113797 none CC1=CC=CC=C1CC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 16, 16, 16, 33, 33, 33, 119, 119, 119, 174, 201, 201, 201, 201, 201, 119, 119, 33, 2, 2, 2, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 16, 33, 33, 33, 33, 119, 174, 174, 201, 201, 33, 33] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 34, 35, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 687 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113797 none CC1=CC=CC=C1CC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 173, 201, 201, 173, 151, 86, 151, 86, 86, 42, 42, 42, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 42, 201, 201, 201, 201, 173, 201, 201, 173, 173, 151, 151, 151, 151, 86, 42, 42, 42, 42, 9, 5, 5, 3, 3, 42, 42] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 815 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113797 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113797/1 /scratch/stefan/7770410/working/building/REAL300020113797 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1207) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1207 `/scratch/stefan/7770410/working/3D/1207' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1CC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113797.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113797/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113797 none CC1=CC=CC=C1CC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 25, 33, 33, 25, 15, 6, 15, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 28, 41, 42, 42, 42, 42, 9, 9, 1, 33, 33, 33, 33, 25, 33, 33, 25, 25, 15, 15, 15, 15, 6, 1, 1, 1, 1, 9, 28, 28, 41, 41, 1, 1] 201 rigid atoms, others: [45, 44, 43, 12, 13, 14, 15, 16, 52, 46, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 310 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113797 none CC1=CC=CC=C1CC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 119, 97, 119, 119, 97, 64, 29, 64, 29, 29, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 9, 119, 119, 119, 119, 97, 119, 119, 97, 97, 64, 64, 64, 64, 29, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [15, 47, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 557 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113797 none CC1=CC=CC=C1CC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 16, 16, 16, 33, 33, 33, 119, 119, 119, 174, 201, 201, 201, 201, 201, 119, 119, 33, 2, 2, 2, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 16, 33, 33, 33, 33, 119, 174, 174, 201, 201, 33, 33] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 34, 35, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 687 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113797 none CC1=CC=CC=C1CC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 172, 201, 201, 172, 151, 86, 151, 86, 86, 42, 42, 42, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 42, 201, 201, 201, 201, 172, 201, 201, 172, 172, 151, 151, 151, 151, 86, 42, 42, 42, 42, 9, 5, 5, 3, 3, 42, 42] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 814 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113797 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113797 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113797/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113797/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113797 Building REAL300020113798 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113798' /scratch/stefan/7770410/working/building/REAL300020113798 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113798 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113798/0 /scratch/stefan/7770410/working/building/REAL300020113798 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1208) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1208 `/scratch/stefan/7770410/working/3D/1208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1) `REAL300020113798.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113798 none CC1(C)CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 32, 45, 47, 47, 47, 47, 11, 11, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 11, 32, 32, 45, 45, 1, 1, 19, 19, 19, 19] 201 rigid atoms, others: [49, 39, 8, 9, 10, 11, 12, 48, 40, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50, 51, 52, 53]) total number of confs: 224 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113798 none CC1(C)CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 91, 91, 30, 30, 30, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 91, 91, 91, 91, 91, 91, 91, 91, 91, 91, 91, 91, 91, 30, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 91, 91, 91, 91] 201 rigid atoms, others: [11, 43, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 265 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113798 none CC1(C)CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 19, 19, 19, 91, 91, 91, 155, 201, 201, 201, 201, 201, 91, 91, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 19, 91, 155, 155, 201, 201, 19, 19, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 50, 51, 52, 53] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 760 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113798 none CC1(C)CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 90, 90, 90, 48, 48, 48, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 48, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 90, 48, 48, 48, 48, 10, 5, 5, 3, 3, 48, 48, 201, 201, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 578 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113798 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113798/1 /scratch/stefan/7770410/working/building/REAL300020113798 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1209) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1209 `/scratch/stefan/7770410/working/3D/1209' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1) `REAL300020113798.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113798 none CC1(C)CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 44, 46, 46, 46, 46, 11, 11, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 11, 31, 31, 44, 44, 1, 1, 19, 19, 19, 19] 201 rigid atoms, others: [49, 39, 8, 9, 10, 11, 12, 48, 40, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50, 51, 52, 53]) total number of confs: 221 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113798 none CC1(C)CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 92, 92, 30, 30, 30, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 30, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 92, 92, 92, 92] 201 rigid atoms, others: [11, 43, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 269 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113798 none CC1(C)CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 19, 19, 19, 92, 92, 92, 155, 201, 201, 201, 201, 201, 92, 92, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 19, 92, 155, 155, 201, 201, 19, 19, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 50, 51, 52, 53] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 755 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113798 none CC1(C)CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 90, 90, 90, 48, 48, 48, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 48, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 90, 48, 48, 48, 48, 10, 5, 5, 3, 3, 48, 48, 201, 201, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 578 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113798 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113798 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113798/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113798/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113798 Building REAL300020113799 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113799' /scratch/stefan/7770410/working/building/REAL300020113799 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113799 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113799/0 /scratch/stefan/7770410/working/building/REAL300020113799 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1210) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1210 `/scratch/stefan/7770410/working/3D/1210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1) `REAL300020113799.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113799 none NC(=O)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 60, 79, 99, 99, 99, 99, 13, 13, 1, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 60, 60, 79, 79, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 44, 10, 11, 12, 13, 14, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 369 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113799 none NC(=O)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 90, 90, 90, 90, 53, 53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 18, 18, 18, 18, 1, 1, 13, 90, 90, 90, 90, 90, 90, 53, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13] 201 rigid atoms, others: [38, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 245 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113799 none NC(=O)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 90, 90, 90, 167, 201, 201, 201, 201, 201, 90, 90, 16, 1, 2, 2, 1, 1, 1, 6, 16, 16, 16, 16, 90, 167, 167, 201, 201, 16, 16] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 27, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 718 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113799 none NC(=O)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 195, 195, 195, 99, 99, 99, 20, 20, 20, 6, 4, 1, 1, 1, 1, 1, 1, 20, 20, 99, 201, 201, 201, 201, 201, 201, 195, 99, 99, 99, 99, 20, 6, 6, 4, 4, 99, 99] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 550 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113799 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113799/1 /scratch/stefan/7770410/working/building/REAL300020113799 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1211) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1211 `/scratch/stefan/7770410/working/3D/1211' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1) `REAL300020113799.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113799 none NC(=O)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 61, 80, 100, 100, 100, 100, 13, 13, 1, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 61, 61, 80, 80, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 44, 10, 11, 12, 13, 14, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 372 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113799 none NC(=O)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 89, 89, 89, 89, 53, 53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 18, 18, 18, 18, 1, 1, 13, 89, 89, 89, 89, 89, 89, 53, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13] 201 rigid atoms, others: [38, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 244 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113799 none NC(=O)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 89, 89, 89, 167, 201, 201, 201, 201, 201, 89, 89, 16, 1, 2, 2, 1, 1, 1, 6, 16, 16, 16, 16, 89, 167, 167, 201, 201, 16, 16] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 27, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 719 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113799 none NC(=O)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 195, 195, 195, 99, 99, 99, 21, 21, 21, 6, 4, 1, 1, 1, 1, 1, 1, 21, 21, 99, 201, 201, 201, 201, 201, 201, 195, 99, 99, 99, 99, 21, 6, 6, 4, 4, 99, 99] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 543 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113799 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113799 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113799/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113799/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113799 Building REAL300020113800 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113800' /scratch/stefan/7770410/working/building/REAL300020113800 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113800 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113800/0 /scratch/stefan/7770410/working/building/REAL300020113800 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1212) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1212 `/scratch/stefan/7770410/working/3D/1212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(CF)C=C1) `REAL300020113800.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113800 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(CF)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 14, 14, 14, 14, 1, 1, 11, 33, 51, 51, 33, 51, 111, 51, 51, 33, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 51, 51, 111, 111, 51, 51] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 541 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113800 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(CF)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [135, 135, 69, 69, 69, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 69, 135, 201, 201, 135, 201, 201, 201, 201, 135, 69, 69, 69, 69, 15, 6, 6, 4, 4, 69, 69, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 841 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113800 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(CF)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 40, 55, 67, 67, 67, 67, 11, 11, 1, 5, 7, 7, 5, 7, 30, 7, 7, 5, 1, 1, 1, 1, 11, 40, 40, 55, 55, 1, 1, 7, 7, 30, 30, 7, 7] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 348 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113800 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(CF)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 7, 7, 7, 51, 51, 51, 138, 178, 201, 201, 201, 201, 51, 51, 7, 1, 1, 1, 1, 1, 7, 1, 1, 3, 7, 7, 7, 7, 51, 138, 138, 178, 178, 7, 7, 1, 1, 7, 7, 1, 1] 201 rigid atoms, others: [1, 39, 40, 43, 44, 19, 20, 21, 22, 23, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 754 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113800 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113800/1 /scratch/stefan/7770410/working/building/REAL300020113800 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1213) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1213 `/scratch/stefan/7770410/working/3D/1213' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(CF)C=C1) `REAL300020113800.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113800/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113800 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(CF)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 13, 13, 13, 13, 1, 1, 11, 33, 52, 52, 33, 52, 112, 52, 52, 33, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 52, 52, 112, 112, 52, 52] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 545 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113800 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(CF)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [135, 135, 70, 70, 70, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 70, 135, 201, 201, 135, 201, 201, 201, 201, 135, 70, 70, 70, 70, 15, 6, 6, 4, 4, 70, 70, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 839 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113800 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(CF)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 38, 53, 66, 66, 66, 66, 11, 11, 1, 5, 8, 8, 5, 8, 31, 8, 8, 5, 1, 1, 1, 1, 11, 38, 38, 53, 53, 1, 1, 8, 8, 31, 31, 8, 8] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 351 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113800 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(CF)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 52, 52, 52, 137, 177, 201, 201, 201, 201, 52, 52, 8, 1, 1, 1, 1, 1, 7, 1, 1, 3, 8, 8, 8, 8, 52, 137, 137, 177, 177, 8, 8, 1, 1, 7, 7, 1, 1] 201 rigid atoms, others: [1, 39, 40, 43, 44, 19, 20, 21, 22, 23, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 752 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113800 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113800 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113800/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113800/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113800 Building REAL300020113801 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113801' /scratch/stefan/7770410/working/building/REAL300020113801 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113801 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113801/0 /scratch/stefan/7770410/working/building/REAL300020113801 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1214) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1214 `/scratch/stefan/7770410/working/3D/1214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC2=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=CC=C2O1) `REAL300020113801.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113801 none CC1=NC2=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 57, 74, 87, 87, 87, 87, 12, 12, 1, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 12, 57, 57, 74, 74, 1, 1, 15, 15, 15] 201 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 332 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113801 none CC1=NC2=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 89, 50, 50, 50, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 12, 89, 89, 89, 89, 89, 89, 89, 89, 50, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 89, 89, 89] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 239 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113801 none CC1=NC2=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 15, 15, 15, 89, 89, 89, 174, 201, 201, 201, 201, 201, 89, 89, 15, 1, 1, 1, 1, 1, 2, 2, 2, 4, 15, 15, 15, 15, 89, 174, 174, 201, 201, 15, 15, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 45, 46, 24, 25, 26, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 723 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113801 none CC1=NC2=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 181, 181, 181, 88, 88, 88, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 88, 201, 201, 201, 201, 201, 201, 201, 201, 181, 88, 88, 88, 88, 18, 6, 6, 4, 4, 88, 88, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 533 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113801 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113801/1 /scratch/stefan/7770410/working/building/REAL300020113801 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1215) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1215 `/scratch/stefan/7770410/working/3D/1215' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC2=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=CC=C2O1) `REAL300020113801.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113801 none CC1=NC2=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 58, 76, 90, 90, 90, 90, 12, 12, 1, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 12, 58, 58, 76, 76, 1, 1, 15, 15, 15] 201 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 343 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113801 none CC1=NC2=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 90, 50, 50, 50, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 12, 90, 90, 90, 90, 90, 90, 90, 90, 50, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 90, 90, 90] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 238 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113801 none CC1=NC2=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 15, 15, 15, 90, 90, 90, 173, 201, 201, 201, 201, 201, 90, 90, 15, 1, 1, 1, 1, 1, 2, 2, 2, 4, 15, 15, 15, 15, 90, 173, 173, 201, 201, 15, 15, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 45, 46, 24, 25, 26, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 719 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113801 none CC1=NC2=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 183, 183, 183, 92, 92, 92, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 92, 201, 201, 201, 201, 201, 201, 201, 201, 183, 92, 92, 92, 92, 17, 6, 6, 4, 4, 92, 92, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 530 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113801 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113801 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113801/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113801/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113801 Building REAL300020113802 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113802' /scratch/stefan/7770410/working/building/REAL300020113802 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113802 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113802/0 /scratch/stefan/7770410/working/building/REAL300020113802 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1216) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1216 `/scratch/stefan/7770410/working/3D/1216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)OC2=CC=C1) `REAL300020113802.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113802 none CC1=C2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)OC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 42, 54, 70, 70, 70, 70, 8, 8, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33, 6, 1, 1, 1, 1, 8, 42, 42, 54, 54, 1, 1, 33, 33, 33] 201 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 280 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113802 none CC1=C2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)OC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 90, 32, 32, 32, 8, 8, 8, 1, 1, 1, 1, 1, 9, 13, 19, 19, 19, 19, 1, 1, 8, 90, 90, 90, 90, 90, 90, 90, 90, 90, 32, 8, 8, 8, 8, 1, 9, 9, 13, 13, 8, 8, 90, 90, 90] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 220 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113802 none CC1=C2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)OC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 33, 33, 33, 90, 90, 90, 176, 201, 201, 201, 201, 201, 90, 90, 33, 1, 1, 1, 1, 1, 2, 2, 2, 1, 10, 33, 33, 33, 33, 90, 176, 176, 201, 201, 33, 33, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 45, 46, 47, 24, 25, 26, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 715 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113802 none CC1=C2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)OC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 156, 156, 156, 79, 79, 79, 23, 23, 23, 6, 4, 1, 1, 1, 1, 1, 1, 23, 23, 79, 201, 201, 201, 201, 201, 201, 201, 201, 201, 156, 79, 79, 79, 79, 23, 6, 6, 4, 4, 79, 79, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 516 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113802 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113802/1 /scratch/stefan/7770410/working/building/REAL300020113802 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1217) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1217 `/scratch/stefan/7770410/working/3D/1217' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)OC2=CC=C1) `REAL300020113802.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113802/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113802 none CC1=C2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)OC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 41, 53, 69, 69, 69, 69, 8, 8, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33, 6, 1, 1, 1, 1, 8, 41, 41, 53, 53, 1, 1, 33, 33, 33] 201 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 274 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113802 none CC1=C2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)OC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 91, 32, 32, 32, 8, 8, 8, 1, 1, 1, 1, 1, 9, 13, 19, 19, 19, 19, 1, 1, 8, 91, 91, 91, 91, 91, 91, 91, 91, 91, 32, 8, 8, 8, 8, 1, 9, 9, 13, 13, 8, 8, 91, 91, 91] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 221 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113802 none CC1=C2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)OC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 33, 33, 33, 91, 91, 91, 176, 201, 201, 201, 201, 201, 91, 91, 33, 1, 1, 1, 1, 1, 2, 2, 2, 1, 10, 33, 33, 33, 33, 91, 176, 176, 201, 201, 33, 33, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 45, 46, 47, 24, 25, 26, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 711 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113802 none CC1=C2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)OC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 156, 156, 156, 78, 78, 78, 23, 23, 23, 6, 4, 1, 1, 1, 1, 1, 1, 23, 23, 78, 201, 201, 201, 201, 201, 201, 201, 201, 201, 156, 78, 78, 78, 78, 23, 6, 6, 4, 4, 78, 78, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 518 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113802 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113802 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113802/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113802/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113802 Building REAL300020113803 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113803' /scratch/stefan/7770410/working/building/REAL300020113803 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113803 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113803/0 /scratch/stefan/7770410/working/building/REAL300020113803 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1218) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1218 `/scratch/stefan/7770410/working/3D/1218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(CC(C)C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113803.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113803 none CCCC(CC(C)C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 89, 34, 89, 111, 111, 111, 34, 34, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 102, 102, 102, 102, 102, 102, 102, 89, 111, 111, 111, 111, 111, 111, 111, 111, 111, 34, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [17, 13, 14, 15, 16, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55]) total number of confs: 557 number of broken/clashed sets: 71 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113803 none CCCC(CC(C)C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 91, 201, 201, 201, 201, 91, 91, 44, 44, 44, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 44, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 91, 44, 44, 44, 44, 12, 6, 6, 4, 4, 44, 44] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 766 number of broken/clashed sets: 83 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113803 none CCCC(CC(C)C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 19, 6, 19, 26, 26, 26, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 30, 45, 51, 51, 51, 51, 11, 11, 1, 24, 24, 24, 24, 24, 24, 24, 19, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 11, 30, 30, 45, 45, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 46, 45, 48, 14, 54, 55, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53]) total number of confs: 327 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113803 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113803/1 /scratch/stefan/7770410/working/building/REAL300020113803 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1219) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1219 `/scratch/stefan/7770410/working/3D/1219' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(CC(C)C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113803.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113803/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113803 none CCCC(CC(C)C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 88, 34, 88, 110, 110, 110, 34, 34, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 101, 101, 101, 101, 101, 101, 101, 88, 110, 110, 110, 110, 110, 110, 110, 110, 110, 34, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [17, 13, 14, 15, 16, 49, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55]) total number of confs: 554 number of broken/clashed sets: 70 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113803 none CCCC(CC(C)C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 89, 201, 201, 201, 201, 89, 89, 43, 43, 43, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 43, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 89, 43, 43, 43, 43, 11, 6, 6, 4, 4, 43, 43] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 774 number of broken/clashed sets: 82 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113803 none CCCC(CC(C)C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 19, 6, 19, 27, 27, 27, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 30, 45, 51, 51, 51, 51, 11, 11, 1, 25, 25, 25, 25, 25, 25, 25, 19, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 11, 30, 30, 45, 45, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 46, 45, 48, 14, 54, 55, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53]) total number of confs: 339 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113803 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113803 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113803/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113803/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113803 Building REAL300020113804 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113804' /scratch/stefan/7770410/working/building/REAL300020113804 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113804 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113804/0 /scratch/stefan/7770410/working/building/REAL300020113804 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1220) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1220 `/scratch/stefan/7770410/working/3D/1220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(C)C) `REAL300020113804.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113804 none CC(=O)NC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 80, 45, 80, 45, 45, 12, 12, 12, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 12, 80, 94, 94, 94, 94, 94, 94, 80, 80, 80, 45, 12, 12, 12, 12, 1, 7, 7, 9, 9, 12, 12, 94, 94, 94, 94, 94, 94, 94] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 500 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113804 none CC(=O)NC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [196, 196, 196, 179, 103, 179, 103, 103, 46, 46, 46, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 46, 179, 195, 195, 196, 196, 196, 196, 179, 179, 179, 103, 46, 46, 46, 46, 8, 4, 4, 2, 2, 46, 46, 195, 195, 195, 195, 195, 195, 195] 196 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 893 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113804 none CC(=O)NC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 11, 6, 11, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 36, 52, 60, 60, 60, 60, 12, 12, 1, 11, 16, 16, 16, 16, 16, 16, 11, 11, 11, 6, 1, 1, 1, 1, 12, 36, 36, 52, 52, 1, 1, 16, 16, 16, 16, 16, 16, 16] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 45, 46, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 319 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113804 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113804/1 /scratch/stefan/7770410/working/building/REAL300020113804 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1221) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1221 `/scratch/stefan/7770410/working/3D/1221' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(C)C) `REAL300020113804.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113804/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113804 none CC(=O)NC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 80, 45, 80, 45, 45, 12, 12, 12, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 12, 80, 95, 95, 95, 95, 95, 95, 80, 80, 80, 45, 12, 12, 12, 12, 1, 7, 7, 9, 9, 12, 12, 95, 95, 95, 95, 95, 95, 95] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 510 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113804 none CC(=O)NC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [197, 197, 197, 180, 102, 180, 102, 102, 45, 45, 45, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 45, 180, 196, 196, 197, 197, 197, 197, 180, 180, 180, 102, 45, 45, 45, 45, 7, 4, 4, 2, 2, 45, 45, 196, 196, 196, 196, 196, 196, 196] 197 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 903 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113804 none CC(=O)NC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 11, 6, 11, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 36, 52, 60, 60, 60, 60, 12, 12, 1, 11, 16, 16, 16, 16, 16, 16, 11, 11, 11, 6, 1, 1, 1, 1, 12, 36, 36, 52, 52, 1, 1, 16, 16, 16, 16, 16, 16, 16] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 45, 46, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 319 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113804 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113804 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113804/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113804/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113804 Building REAL300020113805 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113805' /scratch/stefan/7770410/working/building/REAL300020113805 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113805 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113805/0 /scratch/stefan/7770410/working/building/REAL300020113805 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1222) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1222 `/scratch/stefan/7770410/working/3D/1222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC2CCCCC21) `REAL300020113805.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113805 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC2CCCCC21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 13, 13, 13, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 13, 46, 78, 78, 78, 78, 78, 78, 78, 78, 78, 46, 13, 13, 13, 13, 1, 7, 7, 9, 9, 13, 13, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 272 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113805 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC2CCCCC21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 67, 67, 67, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 67, 151, 201, 201, 201, 201, 201, 201, 201, 201, 201, 151, 67, 67, 67, 67, 12, 6, 6, 4, 4, 67, 67, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 608 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113805 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC2CCCCC21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 39, 58, 66, 66, 66, 66, 13, 13, 1, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 13, 39, 39, 58, 58, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113805 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC2CCCCC21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 12, 12, 12, 78, 78, 78, 151, 201, 201, 201, 201, 201, 78, 78, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 12, 12, 12, 12, 78, 151, 151, 201, 201, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 778 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113805 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113805/1 /scratch/stefan/7770410/working/building/REAL300020113805 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1223) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1223 `/scratch/stefan/7770410/working/3D/1223' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2CCCCC21) `REAL300020113805.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113805 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2CCCCC21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 13, 13, 13, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 13, 46, 78, 78, 78, 78, 78, 78, 78, 78, 78, 46, 13, 13, 13, 13, 1, 7, 7, 9, 9, 13, 13, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 272 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113805 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2CCCCC21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 66, 66, 66, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 66, 151, 201, 201, 201, 201, 201, 201, 201, 201, 201, 151, 66, 66, 66, 66, 11, 6, 6, 4, 4, 66, 66, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 609 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113805 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2CCCCC21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 39, 58, 63, 63, 63, 63, 13, 13, 1, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 13, 39, 39, 58, 58, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 280 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113805 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2CCCCC21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 12, 12, 12, 78, 78, 78, 152, 201, 201, 201, 201, 201, 78, 78, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 12, 12, 12, 12, 78, 152, 152, 201, 201, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 778 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113805 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113805 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113805/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113805/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113805 Building REAL300020113806 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113806' /scratch/stefan/7770410/working/building/REAL300020113806 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113806 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113806/0 /scratch/stefan/7770410/working/building/REAL300020113806 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1224) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1224 `/scratch/stefan/7770410/working/3D/1224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCCCC1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113806.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113806 none CC1(C)CCCCC1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 45, 65, 79, 79, 79, 79, 13, 13, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 13, 45, 45, 65, 65, 1, 1] 201 rigid atoms, others: [11, 44, 10, 43, 12, 13, 14, 45, 52, 46, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 328 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113806 none CC1(C)CCCCC1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 99, 99, 99, 99, 60, 60, 60, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 13, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 60, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13] 201 rigid atoms, others: [13, 14, 47, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 341 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113806 none CC1(C)CCCCC1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 99, 99, 99, 167, 201, 201, 201, 201, 201, 99, 99, 12, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 12, 12, 12, 12, 99, 167, 167, 201, 201, 12, 12] 201 rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 40, 41, 36, 34, 8, 35, 39, 4, 38, 5, 37, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 685 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113806 none CC1(C)CCCCC1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 167, 167, 167, 79, 79, 79, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 79, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 167, 79, 79, 79, 79, 13, 6, 6, 4, 4, 79, 79] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 602 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113806 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113806/1 /scratch/stefan/7770410/working/building/REAL300020113806 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1225) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1225 `/scratch/stefan/7770410/working/3D/1225' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113806.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113806 none CC1(C)CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 45, 65, 79, 79, 79, 79, 13, 13, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 13, 45, 45, 65, 65, 1, 1] 201 rigid atoms, others: [11, 44, 10, 43, 12, 13, 14, 45, 52, 46, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 328 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113806 none CC1(C)CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 99, 99, 99, 99, 60, 60, 60, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 13, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 60, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13] 201 rigid atoms, others: [13, 14, 47, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 341 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113806 none CC1(C)CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 99, 99, 99, 167, 201, 201, 201, 201, 201, 99, 99, 12, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 12, 12, 12, 12, 99, 167, 167, 201, 201, 12, 12] 201 rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 40, 41, 36, 34, 8, 35, 39, 4, 38, 5, 37, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 685 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113806 none CC1(C)CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 167, 167, 167, 79, 79, 79, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 79, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 167, 79, 79, 79, 79, 13, 6, 6, 4, 4, 79, 79] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 602 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113806 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113806 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113806/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113806/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113806 Building REAL300020113807 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113807' /scratch/stefan/7770410/working/building/REAL300020113807 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113807 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113807/0 /scratch/stefan/7770410/working/building/REAL300020113807 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1226) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1226 `/scratch/stefan/7770410/working/3D/1226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(C)(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1) `REAL300020113807.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113807 none CC1CCC(C)(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 6, 16, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 37, 48, 48, 48, 48, 48, 13, 13, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 37, 37, 48, 48, 1, 1, 16, 16, 16, 16] 201 rigid atoms, others: [49, 39, 8, 9, 10, 11, 12, 48, 40, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50, 51, 52, 53]) total number of confs: 224 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113807 none CC1CCC(C)(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 119, 119, 45, 119, 45, 45, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 119, 119, 119, 119, 119, 119, 119, 119, 119, 119, 119, 119, 119, 45, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 119, 119, 119, 119] 201 rigid atoms, others: [11, 43, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 367 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113807 none CC1CCC(C)(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 16, 16, 16, 119, 119, 119, 175, 201, 201, 201, 201, 201, 119, 119, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 16, 16, 16, 16, 119, 175, 175, 201, 201, 16, 16, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 50, 51, 52, 53, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 619 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113807 none CC1CCC(C)(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 90, 201, 90, 90, 49, 49, 49, 9, 9, 9, 5, 2, 1, 1, 1, 1, 1, 1, 9, 9, 49, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 90, 49, 49, 49, 49, 9, 5, 5, 2, 2, 49, 49, 201, 201, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 609 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113807 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113807/1 /scratch/stefan/7770410/working/building/REAL300020113807 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1227) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1227 `/scratch/stefan/7770410/working/3D/1227' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(C)(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1) `REAL300020113807.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113807 none CC1CCC(C)(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 6, 16, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 36, 47, 47, 47, 47, 47, 13, 13, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 36, 36, 47, 47, 1, 1, 16, 16, 16, 16] 201 rigid atoms, others: [49, 39, 8, 9, 10, 11, 12, 48, 40, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50, 51, 52, 53]) total number of confs: 218 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113807 none CC1CCC(C)(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 119, 119, 45, 119, 45, 45, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 119, 119, 119, 119, 119, 119, 119, 119, 119, 119, 119, 119, 119, 45, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 119, 119, 119, 119] 201 rigid atoms, others: [11, 43, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 367 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113807 none CC1CCC(C)(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 16, 16, 16, 119, 119, 119, 175, 201, 201, 201, 201, 201, 119, 119, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 16, 16, 16, 16, 119, 175, 175, 201, 201, 16, 16, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 50, 51, 52, 53, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 619 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113807 none CC1CCC(C)(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 90, 201, 90, 90, 49, 49, 49, 9, 9, 9, 5, 2, 1, 1, 1, 1, 1, 1, 9, 9, 49, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 90, 49, 49, 49, 49, 9, 5, 5, 2, 2, 49, 49, 201, 201, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 607 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113807 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113807 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113807/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113807/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113807 Building REAL300020113808 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113808' /scratch/stefan/7770410/working/building/REAL300020113808 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113808 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113808/0 /scratch/stefan/7770410/working/building/REAL300020113808 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1228) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1228 `/scratch/stefan/7770410/working/3D/1228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113808.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113808 none CC(C)CC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 17, 17, 17, 9, 17, 17, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 27, 40, 40, 40, 40, 40, 8, 8, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 17, 9, 17, 17, 5, 1, 1, 1, 1, 8, 27, 27, 40, 40, 1, 1] 201 rigid atoms, others: [45, 44, 43, 12, 13, 14, 15, 16, 52, 46, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 259 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113808 none CC(C)CC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 72, 72, 72, 41, 72, 72, 24, 24, 24, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 107, 107, 107, 107, 107, 107, 107, 107, 107, 72, 41, 72, 72, 24, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [15, 47, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 447 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113808 none CC(C)CC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 72, 72, 72, 124, 151, 151, 151, 151, 151, 72, 72, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 17, 17, 17, 17, 72, 124, 124, 151, 151, 17, 17] 201 rigid atoms, others: [3, 4, 5, 38, 7, 8, 9, 10, 39, 40, 41, 6] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 563 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113808 none CC(C)CC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 152, 152, 152, 122, 152, 152, 79, 79, 79, 40, 40, 40, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 40, 201, 201, 201, 201, 201, 201, 201, 201, 201, 152, 126, 152, 152, 79, 40, 40, 40, 40, 8, 4, 4, 2, 2, 40, 40] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 719 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113808 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113808/1 /scratch/stefan/7770410/working/building/REAL300020113808 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1229) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1229 `/scratch/stefan/7770410/working/3D/1229' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113808.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113808 none CC(C)CC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 17, 17, 17, 9, 17, 17, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 27, 40, 40, 40, 40, 40, 8, 8, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 17, 9, 17, 17, 5, 1, 1, 1, 1, 8, 27, 27, 40, 40, 1, 1] 201 rigid atoms, others: [45, 44, 43, 12, 13, 14, 15, 16, 52, 46, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 259 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113808 none CC(C)CC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 72, 72, 72, 41, 72, 72, 24, 24, 24, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 107, 107, 107, 107, 107, 107, 107, 107, 107, 72, 41, 72, 72, 24, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [15, 47, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 447 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113808 none CC(C)CC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 72, 72, 72, 124, 151, 151, 151, 151, 151, 72, 72, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 17, 17, 17, 17, 72, 124, 124, 151, 151, 17, 17] 201 rigid atoms, others: [3, 4, 5, 38, 7, 8, 9, 10, 39, 40, 41, 6] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 563 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113808 none CC(C)CC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 152, 152, 152, 122, 152, 152, 79, 79, 79, 40, 40, 40, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 40, 201, 201, 201, 201, 201, 201, 201, 201, 201, 152, 126, 152, 152, 79, 40, 40, 40, 40, 8, 4, 4, 2, 2, 40, 40] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 719 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113808 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113808 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113808/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113808/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113808 Building REAL300020113809 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113809' /scratch/stefan/7770410/working/building/REAL300020113809 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113809 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113809/0 /scratch/stefan/7770410/working/building/REAL300020113809 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1230) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1230 `/scratch/stefan/7770410/working/3D/1230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1) `REAL300020113809.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113809 none NC(=O)C1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 31, 31, 31, 14, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 22, 34, 34, 34, 34, 34, 8, 8, 1, 31, 31, 31, 31, 31, 31, 14, 14, 5, 1, 1, 1, 1, 8, 22, 22, 34, 34, 1, 1, 31, 31] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 218 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113809 none NC(=O)C1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [122, 122, 122, 122, 122, 122, 63, 22, 22, 22, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 122, 122, 122, 122, 122, 122, 63, 63, 22, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8, 122, 122] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 359 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113809 none NC(=O)C1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 13, 13, 13, 31, 31, 31, 122, 122, 122, 163, 201, 201, 201, 201, 201, 122, 122, 31, 1, 1, 2, 2, 1, 1, 4, 4, 13, 31, 31, 31, 31, 122, 163, 163, 201, 201, 31, 31, 1, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 47, 48, 27, 28, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 663 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113809 none NC(=O)C1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 129, 56, 56, 56, 35, 35, 35, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 35, 201, 201, 201, 201, 201, 201, 129, 129, 56, 35, 35, 35, 35, 8, 4, 4, 2, 2, 35, 35, 201, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 621 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113809 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113809/1 /scratch/stefan/7770410/working/building/REAL300020113809 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1231) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1231 `/scratch/stefan/7770410/working/3D/1231' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1) `REAL300020113809.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113809 none NC(=O)C1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 31, 31, 31, 14, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 21, 33, 33, 33, 33, 33, 8, 8, 1, 31, 31, 31, 31, 31, 31, 14, 14, 5, 1, 1, 1, 1, 8, 21, 21, 33, 33, 1, 1, 31, 31] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 215 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113809 none NC(=O)C1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [123, 123, 123, 123, 123, 123, 63, 22, 22, 22, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 123, 123, 123, 123, 123, 123, 63, 63, 22, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8, 123, 123] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 361 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113809 none NC(=O)C1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 13, 13, 13, 31, 31, 31, 123, 123, 123, 163, 201, 201, 201, 201, 201, 123, 123, 31, 1, 1, 2, 2, 1, 1, 4, 4, 13, 31, 31, 31, 31, 123, 163, 163, 201, 201, 31, 31, 1, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 47, 48, 27, 28, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 661 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113809 none NC(=O)C1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 130, 56, 56, 56, 35, 35, 35, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 35, 201, 201, 201, 201, 201, 201, 130, 130, 56, 35, 35, 35, 35, 8, 4, 4, 2, 2, 35, 35, 201, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 623 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113809 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113809 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113809/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113809/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113809 Building REAL300020113810 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113810' /scratch/stefan/7770410/working/building/REAL300020113810 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113810 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113810/0 /scratch/stefan/7770410/working/building/REAL300020113810 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1232) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1232 `/scratch/stefan/7770410/working/3D/1232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C12CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)(C1)C2) `REAL300020113810.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113810 none CC(C)(C)C12CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)(C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 21, 26, 26, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 55, 76, 95, 95, 95, 95, 13, 13, 1, 21, 21, 26, 26, 26, 26, 26, 26, 26, 26, 26, 21, 21, 6, 1, 1, 1, 1, 13, 55, 55, 76, 76, 1, 1, 21, 21, 21, 21] 201 rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 49, 50, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 51, 52, 53, 54]) total number of confs: 399 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113810 none CC(C)(C)C12CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)(C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 96, 100, 100, 96, 96, 51, 51, 51, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 13, 96, 96, 100, 100, 100, 100, 100, 100, 100, 100, 100, 96, 96, 51, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13, 96, 96, 96, 96] 201 rigid atoms, others: [12, 44, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 278 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113810 none CC(C)(C)C12CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)(C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 6, 6, 6, 21, 21, 21, 96, 96, 96, 177, 200, 201, 201, 201, 201, 96, 96, 21, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 6, 21, 21, 21, 21, 96, 177, 177, 200, 200, 21, 21, 1, 1, 1, 1] 201 rigid atoms, others: [1, 4, 5, 6, 7, 38, 51, 52, 53, 54, 26, 27, 37] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 684 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113810 none CC(C)(C)C12CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)(C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 150, 150, 150, 96, 96, 96, 16, 16, 16, 7, 4, 1, 1, 1, 1, 1, 1, 16, 16, 96, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 150, 96, 96, 96, 96, 16, 7, 7, 4, 4, 96, 96, 201, 201, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 543 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113810 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113810/1 /scratch/stefan/7770410/working/building/REAL300020113810 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1233) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1233 `/scratch/stefan/7770410/working/3D/1233' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C12CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)(C1)C2) `REAL300020113810.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113810 none CC(C)(C)C12CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)(C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 21, 26, 26, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 55, 76, 96, 96, 96, 96, 13, 13, 1, 21, 21, 26, 26, 26, 26, 26, 26, 26, 26, 26, 21, 21, 6, 1, 1, 1, 1, 13, 55, 55, 76, 76, 1, 1, 21, 21, 21, 21] 201 rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 49, 50, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 51, 52, 53, 54]) total number of confs: 401 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113810 none CC(C)(C)C12CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)(C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 95, 99, 99, 95, 95, 51, 51, 51, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 13, 95, 95, 99, 99, 99, 99, 99, 99, 99, 99, 99, 95, 95, 51, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13, 95, 95, 95, 95] 201 rigid atoms, others: [12, 44, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 276 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113810 none CC(C)(C)C12CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)(C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 6, 6, 6, 21, 21, 21, 95, 95, 95, 179, 201, 201, 201, 201, 201, 95, 95, 21, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 6, 21, 21, 21, 21, 95, 179, 179, 201, 201, 21, 21, 1, 1, 1, 1] 201 rigid atoms, others: [1, 4, 5, 6, 7, 38, 51, 52, 53, 54, 26, 27, 37] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 686 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113810 none CC(C)(C)C12CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)(C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 149, 149, 149, 97, 97, 97, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 97, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 149, 97, 97, 97, 97, 15, 6, 6, 4, 4, 97, 97, 201, 201, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 535 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113810 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113810 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113810/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113810/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113810 Building REAL300020113811 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113811' /scratch/stefan/7770410/working/building/REAL300020113811 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113811 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113811/0 /scratch/stefan/7770410/working/building/REAL300020113811 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1234) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1234 `/scratch/stefan/7770410/working/3D/1234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@H]1[C@H]2[C@@H]1[C@@H]1CC[C@H]2C1) `REAL300020113811.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113811 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@H]1[C@H]2[C@@H]1[C@@H]1CC[C@H]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 7, 5, 7, 5, 7, 5, 5, 5, 7, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 45, 135, 135, 135, 135, 135, 135, 135, 135, 135, 135, 135, 135, 45, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 135, 135, 135, 135, 135, 135] 201 rigid atoms, others: [37, 6, 7, 8, 9, 16, 17, 5] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 399 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113811 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@H]1[C@H]2[C@@H]1[C@@H]1CC[C@H]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 7, 5, 7, 5, 7, 5, 5, 5, 7, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 42, 42, 42, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 42, 90, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 90, 42, 42, 42, 42, 8, 4, 4, 2, 2, 42, 42, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 595 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113811 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@H]1[C@H]2[C@@H]1[C@@H]1CC[C@H]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 7, 5, 7, 5, 7, 5, 5, 5, 7, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 31, 41, 41, 41, 41, 41, 13, 13, 1, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 1, 1, 1, 1, 13, 31, 31, 41, 41, 1, 1, 28, 28, 28, 28, 28, 28] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 42, 43, 34, 18, 35, 36] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49]) total number of confs: 221 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113811 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@H]1[C@H]2[C@@H]1[C@@H]1CC[C@H]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 7, 5, 7, 5, 7, 5, 5, 5, 7, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 28, 28, 28, 135, 135, 135, 177, 201, 201, 201, 201, 201, 135, 135, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 28, 28, 28, 28, 135, 177, 177, 201, 201, 28, 28, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 571 number of broken/clashed sets: 201 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113811 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113811/1 /scratch/stefan/7770410/working/building/REAL300020113811 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1235) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1235 `/scratch/stefan/7770410/working/3D/1235' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@H]1[C@H]2[C@@H]1[C@@H]1CC[C@H]2C1) `REAL300020113811.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113811 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@H]1[C@H]2[C@@H]1[C@@H]1CC[C@H]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 7, 5, 7, 5, 7, 5, 5, 5, 7, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 45, 135, 135, 135, 135, 135, 135, 135, 135, 135, 135, 135, 135, 45, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 135, 135, 135, 135, 135, 135] 201 rigid atoms, others: [37, 6, 7, 8, 9, 16, 17, 5] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 399 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113811 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@H]1[C@H]2[C@@H]1[C@@H]1CC[C@H]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 7, 5, 7, 5, 7, 5, 5, 5, 7, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 42, 42, 42, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 42, 91, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 91, 42, 42, 42, 42, 8, 4, 4, 2, 2, 42, 42, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 597 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113811 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@H]1[C@H]2[C@@H]1[C@@H]1CC[C@H]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 7, 5, 7, 5, 7, 5, 5, 5, 7, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 31, 41, 41, 41, 41, 41, 13, 13, 1, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 1, 1, 1, 1, 13, 31, 31, 41, 41, 1, 1, 28, 28, 28, 28, 28, 28] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 42, 43, 34, 18, 35, 36] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49]) total number of confs: 221 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113811 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@H]1[C@H]2[C@@H]1[C@@H]1CC[C@H]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 7, 5, 7, 5, 7, 5, 5, 5, 7, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 28, 28, 28, 135, 135, 135, 177, 201, 201, 201, 201, 201, 135, 135, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 28, 28, 28, 28, 135, 177, 177, 201, 201, 28, 28, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 571 number of broken/clashed sets: 201 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113811 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113811 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113811/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113811/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113811 Building REAL300020113812 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113812' /scratch/stefan/7770410/working/building/REAL300020113812 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113812 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113812/0 /scratch/stefan/7770410/working/building/REAL300020113812 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1236) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1236 `/scratch/stefan/7770410/working/3D/1236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2=C(Cl)C=CC=C21) `REAL300020113812.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113812 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2=C(Cl)C=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 16, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 53, 160, 160, 160, 160, 160, 160, 160, 160, 53, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 160, 160, 160, 160, 160, 160] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 453 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113812 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2=C(Cl)C=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 16, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 43, 43, 43, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 43, 102, 201, 201, 201, 201, 201, 201, 201, 201, 102, 43, 43, 43, 43, 8, 4, 4, 2, 2, 43, 43, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 565 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113812 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2=C(Cl)C=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 16, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 31, 42, 42, 42, 42, 42, 13, 13, 1, 6, 44, 44, 44, 44, 44, 44, 44, 44, 6, 1, 1, 1, 1, 13, 31, 31, 42, 42, 1, 1, 44, 44, 44, 44, 44, 44] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113812 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2=C(Cl)C=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 16, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 44, 44, 44, 160, 160, 160, 189, 201, 201, 201, 201, 201, 160, 160, 44, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 44, 44, 44, 44, 160, 189, 189, 201, 201, 44, 44, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 480 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113812 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113812/1 /scratch/stefan/7770410/working/building/REAL300020113812 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1237) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1237 `/scratch/stefan/7770410/working/3D/1237' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2=C(Cl)C=CC=C21) `REAL300020113812.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113812 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2=C(Cl)C=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 16, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 53, 159, 159, 159, 159, 159, 159, 159, 159, 53, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 159, 159, 159, 159, 159, 159] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 451 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113812 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2=C(Cl)C=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 16, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 42, 42, 42, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 42, 101, 201, 201, 201, 201, 201, 201, 201, 201, 101, 42, 42, 42, 42, 8, 4, 4, 2, 2, 42, 42, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 567 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113812 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2=C(Cl)C=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 16, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 30, 41, 41, 41, 41, 41, 13, 13, 1, 6, 44, 44, 44, 44, 44, 44, 44, 44, 6, 1, 1, 1, 1, 13, 30, 30, 41, 41, 1, 1, 44, 44, 44, 44, 44, 44] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113812 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2=C(Cl)C=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 16, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 44, 44, 44, 159, 159, 159, 188, 201, 201, 201, 201, 201, 159, 159, 44, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 44, 44, 44, 44, 159, 188, 188, 201, 201, 44, 44, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 485 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113812 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113812 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113812/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113812/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113812 Building REAL300020113813 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113813' /scratch/stefan/7770410/working/building/REAL300020113813 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113813 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113813/0 /scratch/stefan/7770410/working/building/REAL300020113813 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1238) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1238 `/scratch/stefan/7770410/working/3D/1238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)N1C=CN=C1) `REAL300020113813.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113813 none CC(C)CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)N1C=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 65, 27, 27, 27, 10, 10, 10, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 10, 65, 121, 121, 121, 121, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 27, 10, 10, 10, 10, 1, 5, 5, 7, 7, 10, 10, 121, 121, 121] 201 rigid atoms, others: [12, 10, 11, 44, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 362 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113813 none CC(C)CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)N1C=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 131, 131, 63, 63, 63, 36, 36, 36, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 36, 131, 201, 201, 201, 201, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 63, 36, 36, 36, 36, 7, 4, 4, 2, 2, 36, 36, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 657 number of broken/clashed sets: 18 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113813 none CC(C)CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)N1C=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 25, 39, 39, 39, 39, 39, 10, 10, 1, 15, 36, 36, 36, 36, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 10, 25, 25, 39, 39, 1, 1, 36, 36, 36] 201 rigid atoms, others: [43, 49, 7, 8, 9, 10, 11, 40, 50, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 51, 52, 53]) total number of confs: 244 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113813 none CC(C)CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)N1C=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 8, 1, 8, 17, 17, 17, 36, 36, 36, 121, 121, 121, 172, 201, 201, 201, 201, 201, 121, 121, 36, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8, 17, 36, 36, 36, 36, 121, 172, 172, 201, 201, 36, 36, 1, 1, 1] 201 rigid atoms, others: [4, 51, 52, 53, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 683 number of broken/clashed sets: 17 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113813 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113813/1 /scratch/stefan/7770410/working/building/REAL300020113813 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1239) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1239 `/scratch/stefan/7770410/working/3D/1239' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)N1C=CN=C1) `REAL300020113813.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113813 none CC(C)CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)N1C=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 66, 27, 27, 27, 10, 10, 10, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 10, 66, 121, 121, 121, 121, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 27, 10, 10, 10, 10, 1, 5, 5, 7, 7, 10, 10, 121, 121, 121] 201 rigid atoms, others: [12, 10, 11, 44, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 363 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113813 none CC(C)CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)N1C=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 133, 133, 64, 64, 64, 37, 37, 37, 8, 8, 8, 5, 2, 1, 1, 1, 1, 1, 1, 8, 8, 37, 133, 201, 201, 201, 201, 133, 133, 133, 133, 133, 133, 133, 133, 133, 133, 64, 37, 37, 37, 37, 8, 5, 5, 2, 2, 37, 37, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 662 number of broken/clashed sets: 18 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113813 none CC(C)CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)N1C=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 25, 39, 39, 39, 39, 39, 10, 10, 1, 16, 36, 36, 36, 36, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 10, 25, 25, 39, 39, 1, 1, 36, 36, 36] 201 rigid atoms, others: [43, 49, 7, 8, 9, 10, 11, 40, 50, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 51, 52, 53]) total number of confs: 246 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113813 none CC(C)CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)N1C=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 8, 1, 8, 18, 18, 18, 36, 36, 36, 121, 121, 121, 172, 201, 201, 201, 201, 201, 121, 121, 36, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8, 18, 36, 36, 36, 36, 121, 172, 172, 201, 201, 36, 36, 1, 1, 1] 201 rigid atoms, others: [4, 51, 52, 53, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 683 number of broken/clashed sets: 17 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113813 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113813 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113813/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113813/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113813 Building REAL300020113814 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113814' /scratch/stefan/7770410/working/building/REAL300020113814 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113814 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113814/0 /scratch/stefan/7770410/working/building/REAL300020113814 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1240) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1240 `/scratch/stefan/7770410/working/3D/1240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(C(F)(F)F)=NO1) `REAL300020113814.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113814 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(C(F)(F)F)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 15, 15, 15, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 13, 60, 108, 108, 108, 108, 108, 108, 108, 108, 60, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13, 108] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 276 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113814 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(C(F)(F)F)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 15, 15, 15, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [179, 179, 78, 78, 78, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 78, 179, 201, 201, 201, 201, 201, 201, 201, 201, 179, 78, 78, 78, 78, 13, 6, 6, 4, 4, 78, 78, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 528 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113814 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(C(F)(F)F)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 15, 15, 15, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 47, 66, 78, 78, 78, 78, 13, 13, 1, 6, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 13, 47, 47, 66, 66, 1, 1, 21] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40]) total number of confs: 322 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113814 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(C(F)(F)F)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 15, 15, 15, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 21, 21, 21, 108, 108, 108, 172, 201, 201, 201, 201, 201, 108, 108, 21, 1, 1, 1, 1, 2, 2, 2, 1, 1, 7, 21, 21, 21, 21, 108, 172, 172, 201, 201, 21, 21, 1] 201 rigid atoms, others: [1, 40, 19, 20, 21, 22, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 652 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113814 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113814/1 /scratch/stefan/7770410/working/building/REAL300020113814 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1241) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1241 `/scratch/stefan/7770410/working/3D/1241' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(C(F)(F)F)=NO1) `REAL300020113814.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113814 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(C(F)(F)F)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 15, 15, 15, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 13, 60, 108, 108, 108, 108, 108, 108, 108, 108, 60, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13, 108] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 276 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113814 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(C(F)(F)F)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 15, 15, 15, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [179, 179, 78, 78, 78, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 78, 179, 201, 201, 201, 201, 201, 201, 201, 201, 179, 78, 78, 78, 78, 13, 6, 6, 4, 4, 78, 78, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 528 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113814 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(C(F)(F)F)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 15, 15, 15, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 47, 66, 78, 78, 78, 78, 13, 13, 1, 6, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 13, 47, 47, 66, 66, 1, 1, 21] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40]) total number of confs: 322 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113814 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(C(F)(F)F)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 15, 15, 15, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 21, 21, 21, 108, 108, 108, 172, 201, 201, 201, 201, 201, 108, 108, 21, 1, 1, 1, 1, 2, 2, 2, 1, 1, 7, 21, 21, 21, 21, 108, 172, 172, 201, 201, 21, 21, 1] 201 rigid atoms, others: [1, 40, 19, 20, 21, 22, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 652 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113814 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113814 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113814/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113814/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113814 Building REAL300020113815 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113815' /scratch/stefan/7770410/working/building/REAL300020113815 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113815 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113815/0 /scratch/stefan/7770410/working/building/REAL300020113815 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1242) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1242 `/scratch/stefan/7770410/working/3D/1242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CSC=C1Cl) `REAL300020113815.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113815 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CSC=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 31, 77, 77, 77, 77, 77, 31, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9, 77, 77] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 182 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113815 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CSC=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 52, 52, 52, 12, 12, 12, 7, 4, 1, 1, 1, 1, 1, 1, 12, 12, 52, 92, 201, 201, 201, 201, 201, 92, 52, 52, 52, 52, 12, 7, 7, 4, 4, 52, 52, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 431 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113815 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CSC=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 30, 45, 52, 52, 52, 52, 9, 9, 1, 6, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 9, 30, 30, 45, 45, 1, 1, 17, 17] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 35, 36, 26, 27, 28, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113815 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CSC=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 17, 17, 17, 77, 77, 77, 147, 201, 201, 201, 201, 201, 77, 77, 17, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 17, 77, 147, 147, 201, 201, 17, 17, 1, 1] 201 rigid atoms, others: [1, 37, 38, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 792 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113815 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113815/1 /scratch/stefan/7770410/working/building/REAL300020113815 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1243) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1243 `/scratch/stefan/7770410/working/3D/1243' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CSC=C1Cl) `REAL300020113815.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113815 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CSC=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 31, 77, 77, 77, 77, 77, 31, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9, 77, 77] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 182 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113815 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CSC=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 52, 52, 52, 12, 12, 12, 7, 4, 1, 1, 1, 1, 1, 1, 12, 12, 52, 92, 201, 201, 201, 201, 201, 92, 52, 52, 52, 52, 12, 7, 7, 4, 4, 52, 52, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 431 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113815 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CSC=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 30, 45, 52, 52, 52, 52, 9, 9, 1, 6, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 9, 30, 30, 45, 45, 1, 1, 17, 17] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 35, 36, 26, 27, 28, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113815 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CSC=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 17, 17, 17, 77, 77, 77, 147, 201, 201, 201, 201, 201, 77, 77, 17, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 17, 77, 147, 147, 201, 201, 17, 17, 1, 1] 201 rigid atoms, others: [1, 37, 38, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 792 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113815 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113815 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113815/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113815/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113815 Building REAL300020113816 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113816' /scratch/stefan/7770410/working/building/REAL300020113816 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113816 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113816/0 /scratch/stefan/7770410/working/building/REAL300020113816 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1244) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1244 `/scratch/stefan/7770410/working/3D/1244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN(CC(F)F)C=C1) `REAL300020113816.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113816 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN(CC(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 49, 53, 53, 53, 108, 116, 116, 53, 53, 49, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 108, 108, 116, 53, 53] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 501 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113816 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN(CC(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [123, 123, 54, 54, 54, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 54, 123, 125, 125, 125, 201, 201, 201, 125, 125, 123, 54, 54, 54, 54, 8, 4, 4, 2, 2, 54, 54, 201, 201, 201, 125, 125] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 803 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113816 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN(CC(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 37, 55, 55, 55, 55, 55, 13, 13, 1, 6, 8, 8, 8, 17, 23, 23, 8, 8, 6, 1, 1, 1, 1, 13, 37, 37, 55, 55, 1, 1, 17, 17, 23, 8, 8] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 318 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113816 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN(CC(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 8, 8, 8, 53, 53, 53, 105, 127, 127, 127, 127, 127, 53, 53, 8, 1, 1, 1, 1, 5, 8, 8, 1, 1, 4, 8, 8, 8, 8, 53, 105, 105, 127, 127, 8, 8, 5, 5, 8, 1, 1] 201 rigid atoms, others: [1, 43, 44, 19, 20, 21, 22, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 488 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113816 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113816/1 /scratch/stefan/7770410/working/building/REAL300020113816 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1245) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1245 `/scratch/stefan/7770410/working/3D/1245' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN(CC(F)F)C=C1) `REAL300020113816.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113816 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN(CC(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 49, 53, 53, 53, 108, 116, 116, 53, 53, 49, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 108, 108, 116, 53, 53] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 498 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113816 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN(CC(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [123, 123, 54, 54, 54, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 54, 123, 125, 125, 125, 201, 201, 201, 125, 125, 123, 54, 54, 54, 54, 8, 4, 4, 2, 2, 54, 54, 201, 201, 201, 125, 125] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 803 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113816 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN(CC(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 36, 54, 54, 54, 54, 54, 13, 13, 1, 6, 8, 8, 8, 17, 23, 23, 8, 8, 6, 1, 1, 1, 1, 13, 36, 36, 54, 54, 1, 1, 17, 17, 23, 8, 8] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 315 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113816 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN(CC(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 8, 8, 8, 53, 53, 53, 102, 126, 126, 126, 126, 126, 53, 53, 8, 1, 1, 1, 1, 5, 8, 8, 1, 1, 4, 8, 8, 8, 8, 53, 102, 102, 126, 126, 8, 8, 5, 5, 8, 1, 1] 201 rigid atoms, others: [1, 43, 44, 19, 20, 21, 22, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 485 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113816 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113816 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113816/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113816/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113816 Building REAL300020113817 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113817' /scratch/stefan/7770410/working/building/REAL300020113817 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113817 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113817/0 /scratch/stefan/7770410/working/building/REAL300020113817 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1246) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1246 `/scratch/stefan/7770410/working/3D/1246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NN(C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113817.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113817 none CCC1=NN(C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [36, 19, 19, 19, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 27, 36, 47, 47, 47, 47, 6, 6, 1, 36, 36, 36, 36, 36, 19, 19, 19, 19, 6, 1, 1, 1, 1, 6, 27, 27, 36, 36, 1, 1] 138 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 275 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113817 none CCC1=NN(C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [72, 39, 39, 39, 39, 39, 39, 21, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 8, 12, 17, 17, 17, 17, 1, 1, 6, 72, 72, 72, 72, 72, 39, 39, 39, 39, 21, 6, 6, 6, 6, 1, 8, 8, 12, 12, 6, 6] 138 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 314 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113817 none CCC1=NN(C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 19, 19, 39, 39, 39, 81, 92, 94, 94, 94, 94, 39, 39, 19, 5, 5, 5, 5, 5, 2, 2, 2, 1, 7, 19, 19, 19, 19, 39, 81, 81, 92, 92, 19, 19] 138 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 35] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 360 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113817 none CCC1=NN(C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [139, 95, 95, 95, 95, 95, 95, 85, 85, 85, 50, 50, 50, 22, 22, 22, 6, 4, 1, 1, 1, 1, 1, 1, 22, 22, 50, 139, 139, 139, 139, 139, 95, 95, 95, 95, 85, 50, 50, 50, 50, 22, 6, 6, 4, 4, 50, 50] 139 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 526 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113817 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113817/1 /scratch/stefan/7770410/working/building/REAL300020113817 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1247) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1247 `/scratch/stefan/7770410/working/3D/1247' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NN(C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113817.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113817 none CCC1=NN(C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [36, 19, 19, 19, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 26, 35, 46, 46, 46, 46, 6, 6, 1, 36, 36, 36, 36, 36, 19, 19, 19, 19, 6, 1, 1, 1, 1, 6, 26, 26, 35, 35, 1, 1] 139 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 272 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113817 none CCC1=NN(C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [72, 39, 39, 39, 39, 39, 39, 21, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 8, 12, 17, 17, 17, 17, 1, 1, 6, 72, 72, 72, 72, 72, 39, 39, 39, 39, 21, 6, 6, 6, 6, 1, 8, 8, 12, 12, 6, 6] 139 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 314 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113817 none CCC1=NN(C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 19, 19, 39, 39, 39, 81, 92, 95, 95, 95, 95, 39, 39, 19, 5, 5, 5, 5, 5, 2, 2, 2, 1, 7, 19, 19, 19, 19, 39, 81, 81, 92, 92, 19, 19] 139 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 35] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113817 none CCC1=NN(C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [139, 95, 95, 95, 95, 95, 95, 84, 84, 84, 50, 50, 50, 22, 22, 22, 6, 4, 1, 1, 1, 1, 1, 1, 22, 22, 50, 139, 139, 139, 139, 139, 95, 95, 95, 95, 84, 50, 50, 50, 50, 22, 6, 6, 4, 4, 50, 50] 139 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 522 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113817 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113817 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113817/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113817/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113817 Building REAL300020113818 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113818' /scratch/stefan/7770410/working/building/REAL300020113818 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113818 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113818/0 /scratch/stefan/7770410/working/building/REAL300020113818 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1248) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1248 `/scratch/stefan/7770410/working/3D/1248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C2CC2)CC1) `REAL300020113818.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113818 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 10, 30, 55, 102, 102, 55, 55, 30, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 102, 102, 102, 102, 102, 55, 55, 55, 55] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 361 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113818 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 13, 13, 38, 38, 38, 102, 102, 102, 176, 201, 201, 201, 201, 201, 102, 102, 38, 1, 1, 1, 1, 7, 7, 13, 38, 38, 38, 38, 102, 176, 176, 201, 201, 38, 38, 1, 1, 1, 1, 1, 7, 7, 7, 7] 201 rigid atoms, others: [37, 38, 39, 40, 41, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45]) total number of confs: 671 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113818 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 67, 67, 67, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 67, 94, 147, 201, 201, 147, 147, 94, 67, 67, 67, 67, 14, 6, 6, 4, 4, 67, 67, 201, 201, 201, 201, 201, 147, 147, 147, 147] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 649 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113818 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 28, 41, 42, 42, 42, 42, 10, 10, 1, 6, 14, 38, 38, 14, 14, 6, 1, 1, 1, 1, 10, 28, 28, 41, 41, 1, 1, 38, 38, 38, 38, 38, 14, 14, 14, 14] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 35, 36, 26, 27, 28, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 272 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113818 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 14, 14, 14, 55, 55, 55, 116, 141, 142, 142, 142, 142, 55, 55, 14, 1, 1, 7, 7, 1, 1, 4, 14, 14, 14, 14, 55, 116, 116, 141, 141, 14, 14, 7, 7, 7, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [1, 42, 43, 44, 45, 19, 20, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 518 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113818 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113818/1 /scratch/stefan/7770410/working/building/REAL300020113818 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1249) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1249 `/scratch/stefan/7770410/working/3D/1249' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C2CC2)CC1) `REAL300020113818.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113818/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113818 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 10, 31, 56, 104, 104, 56, 56, 31, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 104, 104, 104, 104, 104, 56, 56, 56, 56] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 367 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113818 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 13, 13, 38, 38, 38, 104, 104, 104, 176, 201, 201, 201, 201, 201, 104, 104, 38, 1, 1, 1, 1, 7, 7, 13, 38, 38, 38, 38, 104, 176, 176, 201, 201, 38, 38, 1, 1, 1, 1, 1, 7, 7, 7, 7] 201 rigid atoms, others: [37, 38, 39, 40, 41, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45]) total number of confs: 667 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113818 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 68, 68, 68, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 68, 95, 147, 201, 201, 147, 147, 95, 68, 68, 68, 68, 15, 6, 6, 4, 4, 68, 68, 201, 201, 201, 201, 201, 147, 147, 147, 147] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 647 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113818 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 28, 41, 42, 42, 42, 42, 10, 10, 1, 6, 14, 38, 38, 14, 14, 6, 1, 1, 1, 1, 10, 28, 28, 41, 41, 1, 1, 38, 38, 38, 38, 38, 14, 14, 14, 14] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 35, 36, 26, 27, 28, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 272 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113818 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 14, 14, 14, 56, 56, 56, 117, 142, 143, 143, 143, 143, 56, 56, 14, 1, 1, 7, 7, 1, 1, 4, 14, 14, 14, 14, 56, 117, 117, 142, 142, 14, 14, 7, 7, 7, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [1, 42, 43, 44, 45, 19, 20, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 522 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113818 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113818 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113818/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113818/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113818 Building REAL300020113819 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113819' /scratch/stefan/7770410/working/building/REAL300020113819 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113819 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113819/0 /scratch/stefan/7770410/working/building/REAL300020113819 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1250) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1250 `/scratch/stefan/7770410/working/3D/1250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(=O)NC(C2CC2)=N1) `REAL300020113819.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113819 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(=O)NC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 7, 25, 49, 49, 49, 49, 49, 49, 112, 112, 49, 25, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7, 49, 49, 112, 112, 112, 112, 112] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 326 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113819 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(=O)NC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 12, 24, 24, 60, 60, 60, 112, 112, 112, 185, 201, 201, 201, 201, 201, 112, 112, 60, 12, 12, 12, 12, 12, 1, 1, 1, 1, 12, 24, 60, 60, 60, 60, 112, 185, 185, 201, 201, 60, 60, 12, 12, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 46, 47, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 691 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113819 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(=O)NC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [135, 135, 65, 65, 65, 25, 25, 25, 6, 4, 1, 1, 1, 1, 1, 1, 25, 25, 65, 135, 162, 162, 162, 162, 162, 162, 201, 201, 162, 135, 65, 65, 65, 65, 25, 6, 6, 4, 4, 65, 65, 162, 162, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 578 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113819 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(=O)NC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 35, 43, 55, 55, 55, 55, 7, 7, 1, 6, 17, 17, 17, 17, 17, 17, 60, 60, 17, 6, 1, 1, 1, 1, 7, 35, 35, 43, 43, 1, 1, 17, 17, 60, 60, 60, 60, 60] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 320 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113819 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(=O)NC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 17, 17, 17, 49, 49, 49, 126, 140, 156, 156, 156, 156, 49, 49, 17, 1, 1, 1, 1, 1, 1, 1, 12, 12, 1, 6, 17, 17, 17, 17, 49, 126, 126, 140, 140, 17, 17, 1, 1, 12, 12, 12, 12, 12] 201 rigid atoms, others: [1, 41, 42, 19, 20, 21, 22, 23, 24, 25, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47]) total number of confs: 541 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113819 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113819/1 /scratch/stefan/7770410/working/building/REAL300020113819 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1251) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1251 `/scratch/stefan/7770410/working/3D/1251' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(=O)NC(C2CC2)=N1) `REAL300020113819.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113819 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(=O)NC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 7, 25, 49, 49, 49, 49, 49, 49, 111, 111, 49, 25, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7, 49, 49, 111, 111, 111, 111, 111] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 324 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113819 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(=O)NC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 12, 24, 24, 59, 59, 59, 111, 111, 111, 185, 201, 201, 201, 201, 201, 111, 111, 59, 12, 12, 12, 12, 12, 1, 1, 1, 1, 12, 24, 59, 59, 59, 59, 111, 185, 185, 201, 201, 59, 59, 12, 12, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 46, 47, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 695 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113819 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(=O)NC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [135, 135, 65, 65, 65, 25, 25, 25, 6, 4, 1, 1, 1, 1, 1, 1, 25, 25, 65, 135, 161, 161, 161, 161, 161, 161, 201, 201, 161, 135, 65, 65, 65, 65, 25, 6, 6, 4, 4, 65, 65, 161, 161, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 580 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113819 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(=O)NC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 35, 43, 56, 56, 56, 56, 7, 7, 1, 6, 17, 17, 17, 17, 17, 17, 59, 59, 17, 6, 1, 1, 1, 1, 7, 35, 35, 43, 43, 1, 1, 17, 17, 59, 59, 59, 59, 59] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 320 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113819 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(=O)NC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 17, 17, 17, 49, 49, 49, 127, 141, 157, 157, 157, 157, 49, 49, 17, 1, 1, 1, 1, 1, 1, 1, 12, 12, 1, 6, 17, 17, 17, 17, 49, 127, 127, 141, 141, 17, 17, 1, 1, 12, 12, 12, 12, 12] 201 rigid atoms, others: [1, 41, 42, 19, 20, 21, 22, 23, 24, 25, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47]) total number of confs: 550 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113819 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113819 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113819/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113819/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113819 Building REAL300020113820 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113820' /scratch/stefan/7770410/working/building/REAL300020113820 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113820 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113820/0 /scratch/stefan/7770410/working/building/REAL300020113820 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1252) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1252 `/scratch/stefan/7770410/working/3D/1252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1) `REAL300020113820.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113820 none COC1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 37, 52, 52, 52, 52, 52, 13, 13, 1, 22, 37, 37, 37, 22, 22, 22, 22, 6, 1, 1, 1, 1, 13, 37, 37, 52, 52, 1, 1, 22, 22] 201 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45]) total number of confs: 288 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113820 none COC1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [141, 118, 118, 118, 50, 50, 50, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 118, 141, 141, 141, 118, 118, 118, 118, 50, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 118, 118] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 414 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113820 none COC1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 8, 8, 8, 22, 22, 22, 118, 118, 118, 182, 201, 201, 201, 201, 201, 118, 118, 22, 1, 4, 4, 4, 1, 1, 1, 1, 8, 22, 22, 22, 22, 118, 182, 182, 201, 201, 22, 22, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 44, 45, 24, 28, 29, 30, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 618 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113820 none COC1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 127, 127, 127, 49, 49, 49, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 49, 201, 201, 201, 201, 201, 201, 201, 201, 127, 49, 49, 49, 49, 8, 4, 4, 2, 2, 49, 49, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 619 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113820 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113820/1 /scratch/stefan/7770410/working/building/REAL300020113820 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1253) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1253 `/scratch/stefan/7770410/working/3D/1253' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1) `REAL300020113820.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113820 none COC1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 37, 52, 52, 52, 52, 52, 13, 13, 1, 22, 37, 37, 37, 22, 22, 22, 22, 6, 1, 1, 1, 1, 13, 37, 37, 52, 52, 1, 1, 22, 22] 201 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45]) total number of confs: 288 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113820 none COC1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [140, 118, 118, 118, 50, 50, 50, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 118, 140, 140, 140, 118, 118, 118, 118, 50, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 118, 118] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 412 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113820 none COC1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 8, 8, 8, 22, 22, 22, 118, 118, 118, 182, 201, 201, 201, 201, 201, 118, 118, 22, 1, 4, 4, 4, 1, 1, 1, 1, 8, 22, 22, 22, 22, 118, 182, 182, 201, 201, 22, 22, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 44, 45, 24, 28, 29, 30, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 618 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113820 none COC1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 127, 127, 127, 50, 50, 50, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 50, 201, 201, 201, 201, 201, 201, 201, 201, 127, 50, 50, 50, 50, 9, 4, 4, 2, 2, 50, 50, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 619 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113820 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113820 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113820/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113820/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113820 Building REAL300020113821 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113821' /scratch/stefan/7770410/working/building/REAL300020113821 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113821 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113821/0 /scratch/stefan/7770410/working/building/REAL300020113821 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1254) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1254 `/scratch/stefan/7770410/working/3D/1254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@H]1CCCC(=O)N1) `REAL300020113821.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113821 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 1, 11, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 57, 145, 145, 145, 145, 145, 145, 145, 57, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 145, 145, 145, 145, 145, 145, 145] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 435 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113821 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 1, 11, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [130, 130, 46, 46, 46, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 46, 130, 201, 201, 201, 201, 201, 201, 201, 130, 46, 46, 46, 46, 8, 4, 4, 2, 2, 46, 46, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 597 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113821 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 1, 11, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 32, 46, 46, 46, 46, 46, 13, 13, 1, 6, 37, 37, 37, 37, 37, 37, 37, 6, 1, 1, 1, 1, 13, 32, 32, 46, 46, 1, 1, 37, 37, 37, 37, 37, 37, 37] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 269 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113821 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 1, 11, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 37, 37, 37, 145, 145, 145, 180, 201, 201, 201, 201, 201, 145, 145, 37, 1, 1, 1, 1, 1, 1, 1, 1, 12, 37, 37, 37, 37, 145, 180, 180, 201, 201, 37, 37, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 39, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 546 number of broken/clashed sets: 3 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113821 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113821/1 /scratch/stefan/7770410/working/building/REAL300020113821 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1255) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1255 `/scratch/stefan/7770410/working/3D/1255' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@H]1CCCC(=O)N1) `REAL300020113821.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113821 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 1, 11, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 57, 144, 144, 144, 144, 144, 144, 144, 57, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 144, 144, 144, 144, 144, 144, 144] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 433 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113821 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 1, 11, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [130, 130, 46, 46, 46, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 46, 130, 201, 201, 201, 201, 201, 201, 201, 130, 46, 46, 46, 46, 8, 4, 4, 2, 2, 46, 46, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 597 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113821 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 1, 11, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 32, 46, 46, 46, 46, 46, 13, 13, 1, 6, 37, 37, 37, 37, 37, 37, 37, 6, 1, 1, 1, 1, 13, 32, 32, 46, 46, 1, 1, 37, 37, 37, 37, 37, 37, 37] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 269 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113821 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 1, 11, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 37, 37, 37, 144, 144, 144, 179, 201, 201, 201, 201, 201, 144, 144, 37, 1, 1, 1, 1, 1, 1, 1, 1, 12, 37, 37, 37, 37, 144, 179, 179, 201, 201, 37, 37, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 39, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 551 number of broken/clashed sets: 3 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113821 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113821 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113821/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113821/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113821 Building REAL300020113822 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113822' /scratch/stefan/7770410/working/building/REAL300020113822 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113822 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113822/0 /scratch/stefan/7770410/working/building/REAL300020113822 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1256) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1256 `/scratch/stefan/7770410/working/3D/1256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=CN=C1COCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113822.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113822 none CN1C=CN=C1COCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 77, 77, 49, 23, 20, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 19, 31, 31, 31, 31, 31, 7, 7, 1, 77, 77, 77, 77, 77, 49, 49, 20, 20, 5, 1, 1, 1, 1, 7, 19, 19, 31, 31, 1, 1] 201 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 377 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113822 none CN1C=CN=C1COCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [149, 149, 149, 149, 149, 123, 73, 71, 18, 18, 18, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 149, 149, 149, 149, 149, 123, 123, 71, 71, 18, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 580 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113822 none CN1C=CN=C1COCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 23, 38, 52, 52, 52, 77, 77, 77, 149, 149, 149, 179, 201, 201, 201, 201, 201, 149, 149, 77, 2, 2, 2, 1, 1, 7, 7, 38, 38, 52, 77, 77, 77, 77, 149, 179, 179, 201, 201, 77, 77] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 677 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113822 none CN1C=CN=C1COCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 193, 142, 90, 24, 24, 24, 24, 24, 24, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 24, 201, 201, 201, 201, 201, 193, 193, 90, 90, 24, 24, 24, 24, 24, 8, 4, 4, 2, 2, 24, 24] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 705 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113822 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113822/1 /scratch/stefan/7770410/working/building/REAL300020113822 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1257) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1257 `/scratch/stefan/7770410/working/3D/1257' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=CN=C1COCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113822.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113822 none CN1C=CN=C1COCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 77, 77, 51, 24, 20, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 19, 31, 31, 31, 31, 31, 7, 7, 1, 77, 77, 77, 77, 77, 51, 51, 20, 20, 5, 1, 1, 1, 1, 7, 19, 19, 31, 31, 1, 1] 201 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 382 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113822 none CN1C=CN=C1COCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 151, 151, 151, 126, 74, 71, 18, 18, 18, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 151, 151, 151, 151, 151, 126, 126, 71, 71, 18, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 592 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113822 none CN1C=CN=C1COCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 23, 39, 52, 52, 52, 77, 77, 77, 151, 151, 151, 180, 201, 201, 201, 201, 201, 151, 151, 77, 2, 2, 2, 1, 1, 7, 7, 39, 39, 52, 77, 77, 77, 77, 151, 180, 180, 201, 201, 77, 77] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 668 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113822 none CN1C=CN=C1COCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 192, 140, 88, 25, 25, 25, 25, 25, 25, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 25, 201, 201, 201, 201, 201, 192, 192, 88, 88, 25, 25, 25, 25, 25, 9, 4, 4, 2, 2, 25, 25] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 702 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113822 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113822 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113822/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113822/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113822 Building REAL300020113823 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113823' /scratch/stefan/7770410/working/building/REAL300020113823 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113823 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113823/0 /scratch/stefan/7770410/working/building/REAL300020113823 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1258) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1258 `/scratch/stefan/7770410/working/3D/1258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1=O) `REAL300020113823.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113823 none CN1CCC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 38, 26, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 21, 26, 27, 27, 27, 27, 7, 7, 1, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 26, 26, 6, 1, 1, 1, 1, 7, 21, 21, 26, 26, 1, 1] 69 rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 47, 48, 40, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 235 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113823 none CN1CCC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 52, 48, 19, 19, 19, 7, 7, 7, 1, 1, 1, 1, 1, 8, 10, 11, 11, 11, 11, 1, 1, 7, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 48, 48, 19, 7, 7, 7, 7, 1, 8, 8, 10, 10, 7, 7] 69 rigid atoms, others: [42, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 221 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113823 none CN1CCC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 26, 26, 26, 38, 38, 38, 52, 52, 52, 67, 69, 69, 69, 69, 69, 52, 52, 38, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 7, 7, 26, 38, 38, 38, 38, 52, 67, 67, 69, 69, 38, 38] 69 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 25, 26, 5, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113823 none CN1CCC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 68, 67, 44, 44, 44, 29, 29, 29, 15, 15, 15, 7, 3, 1, 1, 1, 1, 1, 1, 15, 15, 29, 68, 68, 68, 68, 68, 68, 68, 68, 68, 68, 67, 67, 44, 29, 29, 29, 29, 15, 7, 7, 3, 3, 29, 29] 68 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 241 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113823 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113823/1 /scratch/stefan/7770410/working/building/REAL300020113823 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1259) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1259 `/scratch/stefan/7770410/working/3D/1259' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1=O) `REAL300020113823.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113823 none CN1CCC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 38, 26, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 21, 26, 27, 27, 27, 27, 7, 7, 1, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 26, 26, 6, 1, 1, 1, 1, 7, 21, 21, 26, 26, 1, 1] 69 rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 47, 48, 40, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 235 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113823 none CN1CCC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 52, 48, 19, 19, 19, 7, 7, 7, 1, 1, 1, 1, 1, 8, 10, 11, 11, 11, 11, 1, 1, 7, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 48, 48, 19, 7, 7, 7, 7, 1, 8, 8, 10, 10, 7, 7] 69 rigid atoms, others: [42, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 221 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113823 none CN1CCC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 26, 26, 26, 38, 38, 38, 52, 52, 52, 67, 69, 69, 69, 69, 69, 52, 52, 38, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 7, 7, 26, 38, 38, 38, 38, 52, 67, 67, 69, 69, 38, 38] 69 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 25, 26, 5, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113823 none CN1CCC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 68, 67, 44, 44, 44, 29, 29, 29, 15, 15, 15, 7, 3, 1, 1, 1, 1, 1, 1, 15, 15, 29, 68, 68, 68, 68, 68, 68, 68, 68, 68, 68, 67, 67, 44, 29, 29, 29, 29, 15, 7, 7, 3, 3, 29, 29] 68 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 241 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113823 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113823 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113823/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113823/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113823 Building REAL300020113824 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113824' /scratch/stefan/7770410/working/building/REAL300020113824 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113824 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113824/0 /scratch/stefan/7770410/working/building/REAL300020113824 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1260) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1260 `/scratch/stefan/7770410/working/3D/1260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN2CCCCC2=C1) `REAL300020113824.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113824 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN2CCCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 19, 19, 19, 19, 1, 1, 13, 55, 86, 86, 86, 86, 86, 86, 86, 86, 55, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 86, 86, 86, 86, 86, 86, 86, 86, 86] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 251 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113824 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN2CCCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [194, 194, 117, 117, 117, 23, 23, 23, 6, 4, 1, 1, 1, 1, 1, 1, 23, 23, 117, 194, 201, 201, 201, 201, 201, 201, 201, 201, 194, 117, 117, 117, 117, 23, 6, 6, 4, 4, 117, 117, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 539 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113824 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN2CCCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 69, 93, 115, 115, 115, 115, 13, 13, 1, 6, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 13, 69, 69, 93, 93, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 431 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113824 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN2CCCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 17, 17, 17, 86, 86, 86, 171, 201, 201, 201, 201, 201, 86, 86, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 17, 17, 17, 17, 86, 171, 171, 201, 201, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 694 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113824 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113824/1 /scratch/stefan/7770410/working/building/REAL300020113824 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1261) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1261 `/scratch/stefan/7770410/working/3D/1261' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN2CCCCC2=C1) `REAL300020113824.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113824 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN2CCCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 20, 20, 20, 20, 1, 1, 13, 55, 87, 87, 87, 87, 87, 87, 87, 87, 55, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 87, 87, 87, 87, 87, 87, 87, 87, 87] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 255 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113824 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN2CCCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [194, 194, 117, 117, 117, 22, 22, 22, 6, 4, 1, 1, 1, 1, 1, 1, 22, 22, 117, 194, 201, 201, 201, 201, 201, 201, 201, 201, 194, 117, 117, 117, 117, 22, 6, 6, 4, 4, 117, 117, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 540 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113824 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN2CCCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 69, 93, 116, 116, 116, 116, 13, 13, 1, 6, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 13, 69, 69, 93, 93, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 434 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113824 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN2CCCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 18, 18, 18, 87, 87, 87, 171, 201, 201, 201, 201, 201, 87, 87, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 18, 18, 18, 18, 87, 171, 171, 201, 201, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 694 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113824 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113824 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113824/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113824/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113824 Building REAL300020113825 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113825' /scratch/stefan/7770410/working/building/REAL300020113825 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113825 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113825/0 /scratch/stefan/7770410/working/building/REAL300020113825 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1262) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1262 `/scratch/stefan/7770410/working/3D/1262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113825.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113825 none CC(C)(C)C1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 8, 8, 8, 6, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 25, 34, 38, 38, 38, 38, 6, 6, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 8, 8, 6, 1, 1, 1, 1, 6, 25, 25, 34, 34, 1, 1] 77 rigid atoms, others: [45, 44, 43, 12, 13, 14, 15, 16, 52, 46, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 163 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113825 none CC(C)(C)C1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 26, 26, 21, 26, 26, 21, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 9, 12, 14, 14, 14, 14, 1, 1, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 21, 26, 26, 21, 6, 6, 6, 6, 1, 9, 9, 12, 12, 6, 6] 77 rigid atoms, others: [15, 47, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 127 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113825 none CC(C)(C)C1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 26, 26, 26, 58, 77, 77, 77, 77, 77, 26, 26, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 8, 8, 8, 8, 26, 58, 58, 77, 77, 8, 8] 77 rigid atoms, others: [1, 4, 5, 38, 7, 8, 9, 10, 39, 40, 41, 6] set([0, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 318 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113825 none CC(C)(C)C1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 77, 77, 77, 75, 77, 77, 75, 75, 75, 39, 39, 39, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 39, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 75, 77, 77, 75, 39, 39, 39, 39, 17, 6, 6, 4, 4, 39, 39] 77 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 219 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113825 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113825/1 /scratch/stefan/7770410/working/building/REAL300020113825 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1263) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1263 `/scratch/stefan/7770410/working/3D/1263' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113825.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113825 none CC(C)(C)C1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 8, 8, 8, 6, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 25, 34, 38, 38, 38, 38, 6, 6, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 8, 8, 6, 1, 1, 1, 1, 6, 25, 25, 34, 34, 1, 1] 77 rigid atoms, others: [45, 44, 43, 12, 13, 14, 15, 16, 52, 46, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 163 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113825 none CC(C)(C)C1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 26, 26, 21, 26, 26, 21, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 9, 12, 14, 14, 14, 14, 1, 1, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 21, 26, 26, 21, 6, 6, 6, 6, 1, 9, 9, 12, 12, 6, 6] 77 rigid atoms, others: [15, 47, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 127 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113825 none CC(C)(C)C1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 26, 26, 26, 58, 77, 77, 77, 77, 77, 26, 26, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 8, 8, 8, 8, 26, 58, 58, 77, 77, 8, 8] 77 rigid atoms, others: [1, 4, 5, 38, 7, 8, 9, 10, 39, 40, 41, 6] set([0, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 318 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113825 none CC(C)(C)C1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 77, 77, 77, 75, 77, 77, 75, 75, 75, 39, 39, 39, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 39, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 75, 77, 77, 75, 39, 39, 39, 39, 17, 6, 6, 4, 4, 39, 39] 77 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 219 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113825 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113825 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113825/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113825/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113825 Building REAL300020113826 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113826' /scratch/stefan/7770410/working/building/REAL300020113826 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113826 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113826/0 /scratch/stefan/7770410/working/building/REAL300020113826 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1264) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1264 `/scratch/stefan/7770410/working/3D/1264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=C(C2CC2)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113826.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113826 none CCN1N=C(C2CC2)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 9, 9, 9, 1, 1, 1, 1, 9, 9, 9, 19, 19, 19, 40, 40, 40, 116, 116, 116, 163, 201, 201, 201, 201, 201, 116, 116, 40, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 9, 19, 40, 40, 40, 40, 116, 163, 163, 201, 201, 40, 40] 201 rigid atoms, others: [34, 35, 4, 5, 6, 7, 36, 38, 37] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 733 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113826 none CCN1N=C(C2CC2)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [185, 124, 124, 124, 124, 124, 201, 201, 124, 84, 84, 84, 40, 40, 40, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 40, 185, 185, 185, 185, 185, 201, 201, 201, 201, 201, 124, 84, 40, 40, 40, 40, 10, 6, 6, 4, 4, 40, 40] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 944 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113826 none CCN1N=C(C2CC2)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 12, 12, 12, 12, 12, 40, 40, 12, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 24, 36, 36, 36, 36, 36, 7, 7, 1, 20, 20, 20, 20, 20, 40, 40, 40, 40, 40, 12, 5, 1, 1, 1, 1, 7, 24, 24, 36, 36, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 284 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113826 none CCN1N=C(C2CC2)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 9, 9, 1, 1, 1, 4, 4, 4, 12, 12, 12, 55, 55, 55, 87, 116, 116, 116, 116, 116, 55, 55, 12, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 1, 4, 12, 12, 12, 12, 55, 87, 87, 116, 116, 12, 12] 201 rigid atoms, others: [1, 2, 3, 4, 5, 39, 8, 9, 10] set([0, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 447 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113826 none CCN1N=C(C2CC2)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 55, 55, 55, 55, 55, 116, 116, 55, 24, 24, 24, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 88, 88, 88, 88, 88, 116, 116, 116, 116, 116, 55, 24, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 529 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113826 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113826/1 /scratch/stefan/7770410/working/building/REAL300020113826 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1265) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1265 `/scratch/stefan/7770410/working/3D/1265' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=C(C2CC2)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113826.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113826 none CCN1N=C(C2CC2)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 9, 9, 9, 1, 1, 1, 1, 9, 9, 9, 19, 19, 19, 42, 42, 42, 117, 117, 117, 163, 201, 201, 201, 201, 201, 117, 117, 42, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 9, 19, 42, 42, 42, 42, 117, 163, 163, 201, 201, 42, 42] 201 rigid atoms, others: [34, 35, 4, 5, 6, 7, 36, 38, 37] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 729 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113826 none CCN1N=C(C2CC2)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [185, 126, 126, 126, 126, 126, 201, 201, 126, 85, 85, 85, 41, 41, 41, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 41, 185, 185, 185, 185, 185, 201, 201, 201, 201, 201, 126, 85, 41, 41, 41, 41, 11, 6, 6, 4, 4, 41, 41] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 930 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113826 none CCN1N=C(C2CC2)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 13, 13, 13, 13, 13, 42, 42, 13, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 23, 35, 35, 35, 35, 35, 7, 7, 1, 20, 20, 20, 20, 20, 42, 42, 42, 42, 42, 13, 5, 1, 1, 1, 1, 7, 23, 23, 35, 35, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 283 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113826 none CCN1N=C(C2CC2)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 9, 9, 1, 1, 1, 4, 4, 4, 13, 13, 13, 57, 57, 57, 88, 117, 117, 117, 117, 117, 57, 57, 13, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 1, 4, 13, 13, 13, 13, 57, 88, 88, 117, 117, 13, 13] 201 rigid atoms, others: [1, 2, 3, 4, 5, 39, 8, 9, 10] set([0, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 444 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113826 none CCN1N=C(C2CC2)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 57, 57, 57, 57, 57, 117, 117, 57, 24, 24, 24, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 89, 89, 89, 89, 89, 117, 117, 117, 117, 117, 57, 24, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 527 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113826 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113826 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113826/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113826/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113826 Building REAL300020113827 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113827' /scratch/stefan/7770410/working/building/REAL300020113827 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113827 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113827/0 /scratch/stefan/7770410/working/building/REAL300020113827 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1266) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1266 `/scratch/stefan/7770410/working/3D/1266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113827.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113827 none COCCN1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 25, 25, 11, 11, 11, 11, 11, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 21, 33, 33, 33, 33, 33, 8, 8, 1, 38, 38, 38, 25, 25, 25, 25, 11, 11, 5, 1, 1, 1, 1, 8, 21, 21, 33, 33, 1, 1] 201 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 248 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113827 none COCCN1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 96, 96, 56, 56, 56, 56, 56, 26, 26, 26, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 114, 114, 114, 96, 96, 96, 96, 56, 56, 26, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 377 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113827 none COCCN1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 56, 56, 56, 101, 142, 142, 142, 142, 142, 56, 56, 11, 8, 8, 8, 4, 4, 4, 4, 1, 1, 4, 11, 11, 11, 11, 56, 101, 101, 142, 142, 11, 11] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 35, 36] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 576 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113827 none COCCN1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 147, 147, 147, 147, 147, 64, 64, 64, 35, 35, 35, 10, 10, 10, 5, 2, 1, 1, 1, 1, 1, 1, 10, 10, 35, 201, 201, 201, 201, 201, 201, 201, 147, 147, 64, 35, 35, 35, 35, 10, 5, 5, 2, 2, 35, 35] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 600 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113827 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113827/1 /scratch/stefan/7770410/working/building/REAL300020113827 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1267) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1267 `/scratch/stefan/7770410/working/3D/1267' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113827.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113827 none COCCN1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 25, 25, 11, 11, 11, 11, 11, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 21, 33, 33, 33, 33, 33, 8, 8, 1, 38, 38, 38, 25, 25, 25, 25, 11, 11, 5, 1, 1, 1, 1, 8, 21, 21, 33, 33, 1, 1] 201 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 248 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113827 none COCCN1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 96, 96, 56, 56, 56, 56, 56, 26, 26, 26, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 115, 115, 115, 96, 96, 96, 96, 56, 56, 26, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 379 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113827 none COCCN1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 56, 56, 56, 100, 141, 141, 141, 141, 141, 56, 56, 11, 8, 8, 8, 4, 4, 4, 4, 1, 1, 4, 11, 11, 11, 11, 56, 100, 100, 141, 141, 11, 11] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 35, 36] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 570 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113827 none COCCN1N=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 145, 145, 145, 145, 145, 62, 62, 62, 34, 34, 34, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 34, 201, 201, 201, 201, 201, 201, 201, 145, 145, 62, 34, 34, 34, 34, 9, 4, 4, 2, 2, 34, 34] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 605 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113827 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113827 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113827/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113827/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113827 Building REAL300020113828 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113828' /scratch/stefan/7770410/working/building/REAL300020113828 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113828 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113828/0 /scratch/stefan/7770410/working/building/REAL300020113828 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1268) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1268 `/scratch/stefan/7770410/working/3D/1268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN2N=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)N=C2N=C1) `REAL300020113828.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113828 none CC1=CN2N=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)N=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 44, 60, 71, 71, 71, 71, 11, 11, 1, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 11, 44, 44, 60, 60, 1, 1, 19] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45]) total number of confs: 289 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113828 none CC1=CN2N=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)N=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 93, 93, 44, 44, 44, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 1, 1, 11, 93, 93, 93, 93, 93, 93, 93, 93, 44, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 93] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 236 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113828 none CC1=CN2N=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)N=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 19, 93, 93, 93, 154, 201, 201, 201, 201, 201, 93, 93, 19, 1, 1, 1, 1, 2, 2, 2, 1, 5, 19, 19, 19, 19, 93, 154, 154, 201, 201, 19, 19, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 45, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 733 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113828 none CC1=CN2N=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)N=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 127, 127, 127, 71, 71, 71, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 71, 201, 201, 201, 201, 201, 201, 201, 201, 127, 71, 71, 71, 71, 14, 6, 6, 4, 4, 71, 71, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 492 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113828 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113828/1 /scratch/stefan/7770410/working/building/REAL300020113828 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1269) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1269 `/scratch/stefan/7770410/working/3D/1269' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN2N=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)N=C2N=C1) `REAL300020113828.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113828/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113828 none CC1=CN2N=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)N=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 44, 60, 71, 71, 71, 71, 11, 11, 1, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 11, 44, 44, 60, 60, 1, 1, 19] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45]) total number of confs: 289 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113828 none CC1=CN2N=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)N=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 93, 93, 44, 44, 44, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 1, 1, 11, 93, 93, 93, 93, 93, 93, 93, 93, 44, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 93] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 236 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113828 none CC1=CN2N=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)N=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 19, 93, 93, 93, 154, 201, 201, 201, 201, 201, 93, 93, 19, 1, 1, 1, 1, 2, 2, 2, 1, 5, 19, 19, 19, 19, 93, 154, 154, 201, 201, 19, 19, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 45, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 733 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113828 none CC1=CN2N=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)N=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 127, 127, 127, 71, 71, 71, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 71, 201, 201, 201, 201, 201, 201, 201, 201, 127, 71, 71, 71, 71, 14, 6, 6, 4, 4, 71, 71, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 492 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113828 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113828 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113828/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113828/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113828 Building REAL300020113829 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113829' /scratch/stefan/7770410/working/building/REAL300020113829 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113829 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113829/0 /scratch/stefan/7770410/working/building/REAL300020113829 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1270) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1270 `/scratch/stefan/7770410/working/3D/1270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113829.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113829 none CC1=CN=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 6, 20, 20, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 27, 40, 44, 44, 44, 44, 11, 11, 1, 20, 20, 20, 20, 20, 20, 5, 1, 1, 1, 1, 11, 27, 27, 40, 40, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 214 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113829 none CC1=CN=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 63, 90, 90, 30, 30, 30, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 90, 90, 90, 90, 90, 90, 30, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [37, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 240 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113829 none CC1=CN=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 20, 20, 20, 90, 90, 90, 152, 201, 201, 201, 201, 201, 90, 90, 20, 2, 2, 2, 1, 1, 1, 10, 20, 20, 20, 20, 90, 152, 152, 201, 201, 20, 20] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 780 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113829 none CC1=CN=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 87, 87, 87, 46, 46, 46, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 46, 201, 201, 201, 201, 201, 201, 87, 46, 46, 46, 46, 12, 6, 6, 4, 4, 46, 46] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 413 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113829 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113829/1 /scratch/stefan/7770410/working/building/REAL300020113829 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1271) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1271 `/scratch/stefan/7770410/working/3D/1271' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113829.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113829/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113829 none CC1=CN=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 6, 20, 20, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 27, 40, 44, 44, 44, 44, 11, 11, 1, 20, 20, 20, 20, 20, 20, 5, 1, 1, 1, 1, 11, 27, 27, 40, 40, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 214 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113829 none CC1=CN=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 64, 90, 90, 30, 30, 30, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 90, 90, 90, 90, 90, 90, 30, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [37, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 241 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113829 none CC1=CN=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 20, 20, 20, 90, 90, 90, 152, 201, 201, 201, 201, 201, 90, 90, 20, 2, 2, 2, 1, 1, 1, 10, 20, 20, 20, 20, 90, 152, 152, 201, 201, 20, 20] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 779 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113829 none CC1=CN=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 87, 87, 87, 46, 46, 46, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 46, 201, 201, 201, 201, 201, 201, 87, 46, 46, 46, 46, 12, 6, 6, 4, 4, 46, 46] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 412 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113829 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113829 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113829/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113829/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113829 Building REAL300020113830 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113830' /scratch/stefan/7770410/working/building/REAL300020113830 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113830 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113830/0 /scratch/stefan/7770410/working/building/REAL300020113830 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1272) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1272 `/scratch/stefan/7770410/working/3D/1272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CC=C2O1) `REAL300020113830.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113830 none CC1=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 31, 45, 51, 51, 51, 51, 9, 9, 1, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 9, 31, 31, 45, 45, 1, 1, 13, 13] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46]) total number of confs: 218 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113830 none CC1=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 72, 72, 27, 27, 27, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 72, 72, 72, 72, 72, 72, 72, 72, 27, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 72, 72] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 169 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113830 none CC1=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 72, 72, 72, 147, 201, 201, 201, 201, 201, 72, 72, 13, 1, 1, 1, 1, 2, 2, 2, 1, 5, 13, 13, 13, 13, 72, 147, 147, 201, 201, 13, 13, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 45, 46, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 820 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113830 none CC1=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 88, 88, 88, 52, 52, 52, 11, 11, 11, 7, 4, 1, 1, 1, 1, 1, 1, 11, 11, 52, 201, 201, 201, 201, 201, 201, 201, 201, 88, 52, 52, 52, 52, 11, 7, 7, 4, 4, 52, 52, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 422 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113830 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113830/1 /scratch/stefan/7770410/working/building/REAL300020113830 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1273) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1273 `/scratch/stefan/7770410/working/3D/1273' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CC=C2O1) `REAL300020113830.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113830/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113830 none CC1=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 30, 44, 50, 50, 50, 50, 9, 9, 1, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 9, 30, 30, 44, 44, 1, 1, 13, 13] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46]) total number of confs: 215 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113830 none CC1=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 72, 72, 26, 26, 26, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 72, 72, 72, 72, 72, 72, 72, 72, 26, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 72, 72] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 168 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113830 none CC1=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 72, 72, 72, 147, 201, 201, 201, 201, 201, 72, 72, 13, 1, 1, 1, 1, 2, 2, 2, 1, 5, 13, 13, 13, 13, 72, 147, 147, 201, 201, 13, 13, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 45, 46, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 820 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113830 none CC1=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 88, 88, 88, 52, 52, 52, 11, 11, 11, 7, 4, 1, 1, 1, 1, 1, 1, 11, 11, 52, 201, 201, 201, 201, 201, 201, 201, 201, 88, 52, 52, 52, 52, 11, 7, 7, 4, 4, 52, 52, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 422 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113830 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113830 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113830/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113830/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113830 Building REAL300020113831 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113831' /scratch/stefan/7770410/working/building/REAL300020113831 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113831 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113831/0 /scratch/stefan/7770410/working/building/REAL300020113831 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1274) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1274 `/scratch/stefan/7770410/working/3D/1274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2C=CNC2=C1) `REAL300020113831.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113831 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2C=CNC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 27, 74, 74, 74, 74, 74, 74, 74, 74, 27, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9, 74, 74, 74, 74, 74] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 174 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113831 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2C=CNC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 51, 51, 51, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 51, 91, 201, 201, 201, 201, 201, 201, 201, 201, 91, 51, 51, 51, 51, 11, 6, 6, 4, 4, 51, 51, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 429 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113831 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2C=CNC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 31, 45, 51, 51, 51, 51, 9, 9, 1, 6, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 9, 31, 31, 45, 45, 1, 1, 15, 15, 15, 15, 15] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113831 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2C=CNC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 15, 15, 15, 74, 74, 74, 156, 201, 201, 201, 201, 201, 74, 74, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 74, 156, 156, 201, 201, 15, 15, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 804 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113831 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113831/1 /scratch/stefan/7770410/working/building/REAL300020113831 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1275) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1275 `/scratch/stefan/7770410/working/3D/1275' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2C=CNC2=C1) `REAL300020113831.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113831/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113831 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2C=CNC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 27, 74, 74, 74, 74, 74, 74, 74, 74, 27, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9, 74, 74, 74, 74, 74] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 174 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113831 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2C=CNC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 51, 51, 51, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 51, 91, 201, 201, 201, 201, 201, 201, 201, 201, 91, 51, 51, 51, 51, 11, 6, 6, 4, 4, 51, 51, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 429 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113831 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2C=CNC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 31, 45, 51, 51, 51, 51, 9, 9, 1, 6, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 9, 31, 31, 45, 45, 1, 1, 15, 15, 15, 15, 15] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113831 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2C=CNC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 15, 15, 15, 74, 74, 74, 156, 201, 201, 201, 201, 201, 74, 74, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 74, 156, 156, 201, 201, 15, 15, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 804 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113831 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113831 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113831/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113831/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113831 Building REAL300020113832 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113832' /scratch/stefan/7770410/working/building/REAL300020113832 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113832 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113832/0 /scratch/stefan/7770410/working/building/REAL300020113832 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1276) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1276 `/scratch/stefan/7770410/working/3D/1276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CNN=C2N=C1) `REAL300020113832.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113832 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CNN=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 8, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 27, 73, 73, 73, 73, 73, 73, 73, 73, 27, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 73, 73, 73, 73] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 169 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113832 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CNN=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 8, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 50, 50, 50, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 50, 89, 201, 201, 201, 201, 201, 201, 201, 201, 89, 50, 50, 50, 50, 10, 6, 6, 4, 4, 50, 50, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 433 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113832 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CNN=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 8, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 30, 44, 50, 50, 50, 50, 9, 9, 1, 6, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 9, 30, 30, 44, 44, 1, 1, 15, 15, 15, 15] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113832 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CNN=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 8, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 15, 15, 15, 73, 73, 73, 151, 201, 201, 201, 201, 201, 73, 73, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 73, 151, 151, 201, 201, 15, 15, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 810 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113832 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113832/1 /scratch/stefan/7770410/working/building/REAL300020113832 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1277) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1277 `/scratch/stefan/7770410/working/3D/1277' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CNN=C2N=C1) `REAL300020113832.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113832/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113832 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CNN=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 8, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 27, 73, 73, 73, 73, 73, 73, 73, 73, 27, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 73, 73, 73, 73] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 169 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113832 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CNN=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 8, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 51, 51, 51, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 51, 87, 201, 201, 201, 201, 201, 201, 201, 201, 87, 51, 51, 51, 51, 11, 6, 6, 4, 4, 51, 51, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 429 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113832 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CNN=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 8, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 30, 44, 50, 50, 50, 50, 9, 9, 1, 6, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 9, 30, 30, 44, 44, 1, 1, 15, 15, 15, 15] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113832 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CNN=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 8, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 15, 15, 15, 73, 73, 73, 151, 201, 201, 201, 201, 201, 73, 73, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 73, 151, 151, 201, 201, 15, 15, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 810 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113832 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113832 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113832/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113832/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113832 Building REAL300020113833 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113833' /scratch/stefan/7770410/working/building/REAL300020113833 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113833 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113833/0 /scratch/stefan/7770410/working/building/REAL300020113833 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1278) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1278 `/scratch/stefan/7770410/working/3D/1278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC1(F)F) `REAL300020113833.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113833 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC1(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 54, 144, 144, 144, 144, 144, 54, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 144, 144, 144, 144, 144] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 429 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113833 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC1(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 49, 49, 49, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 49, 128, 201, 201, 201, 201, 201, 128, 49, 49, 49, 49, 8, 4, 4, 2, 2, 49, 49, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 611 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113833 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC1(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 35, 49, 49, 49, 49, 49, 13, 13, 1, 6, 31, 31, 31, 31, 31, 6, 1, 1, 1, 1, 13, 35, 35, 49, 49, 1, 1, 31, 31, 31, 31, 31] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 35, 36, 26, 27, 28, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113833 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC1(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 31, 31, 31, 144, 144, 144, 186, 201, 201, 201, 201, 201, 144, 144, 31, 1, 1, 1, 1, 1, 1, 10, 31, 31, 31, 31, 144, 186, 186, 201, 201, 31, 31, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 37, 38, 39, 40, 41, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 528 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113833 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113833/1 /scratch/stefan/7770410/working/building/REAL300020113833 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1279) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1279 `/scratch/stefan/7770410/working/3D/1279' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC1(F)F) `REAL300020113833.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113833/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113833 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC1(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 54, 144, 144, 144, 144, 144, 54, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 144, 144, 144, 144, 144] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 429 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113833 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC1(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 50, 50, 50, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 50, 128, 201, 201, 201, 201, 201, 128, 50, 50, 50, 50, 9, 4, 4, 2, 2, 50, 50, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 609 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113833 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC1(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 35, 49, 49, 49, 49, 49, 13, 13, 1, 6, 31, 31, 31, 31, 31, 6, 1, 1, 1, 1, 13, 35, 35, 49, 49, 1, 1, 31, 31, 31, 31, 31] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 35, 36, 26, 27, 28, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113833 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC1(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 31, 31, 31, 144, 144, 144, 186, 201, 201, 201, 201, 201, 144, 144, 31, 1, 1, 1, 1, 1, 1, 10, 31, 31, 31, 31, 144, 186, 186, 201, 201, 31, 31, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 37, 38, 39, 40, 41, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 528 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113833 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113833 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113833/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113833/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113833 Building REAL300020113834 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113834' /scratch/stefan/7770410/working/building/REAL300020113834 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113834 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113834/0 /scratch/stefan/7770410/working/building/REAL300020113834 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1280) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1280 `/scratch/stefan/7770410/working/3D/1280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NSC=C1) `REAL300020113834.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113834 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NSC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 3, 6, 10, 10, 10, 10, 6, 3, 3, 3, 3, 1, 5, 5, 5, 5, 3, 3, 10, 10] 11 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 29] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113834 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NSC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 5, 5, 5, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 11, 11, 11, 11, 8, 5, 5, 5, 5, 5, 3, 3, 1, 1, 5, 5, 11, 11] 11 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 29 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113834 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NSC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 3, 3, 1, 6, 10, 10, 10, 10, 6, 1, 1, 1, 1, 3, 5, 5, 5, 5, 1, 1, 10, 10] 11 rigid atoms, others: [2, 3, 4, 5, 6, 34, 18, 35, 25, 26, 27, 28] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113834 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NSC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 10, 10, 10, 1, 1, 1, 1, 1, 6, 10, 10, 10, 10, 10, 11, 11, 11, 11, 10, 10, 1, 1] 11 rigid atoms, others: [1, 36, 37, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 31 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113834 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113834/1 /scratch/stefan/7770410/working/building/REAL300020113834 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1281) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1281 `/scratch/stefan/7770410/working/3D/1281' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NSC=C1) `REAL300020113834.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113834 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NSC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 3, 6, 10, 10, 10, 10, 6, 3, 3, 3, 3, 1, 5, 5, 5, 5, 3, 3, 10, 10] 11 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 29] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113834 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NSC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 5, 5, 5, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 11, 11, 11, 11, 8, 5, 5, 5, 5, 5, 3, 3, 1, 1, 5, 5, 11, 11] 11 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 29 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113834 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NSC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 3, 3, 1, 6, 10, 10, 10, 10, 6, 1, 1, 1, 1, 3, 5, 5, 5, 5, 1, 1, 10, 10] 11 rigid atoms, others: [2, 3, 4, 5, 6, 34, 18, 35, 25, 26, 27, 28] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113834 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NSC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 10, 10, 10, 1, 1, 1, 1, 1, 6, 10, 10, 10, 10, 10, 11, 11, 11, 11, 10, 10, 1, 1] 11 rigid atoms, others: [1, 36, 37, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 31 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113834 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113834 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113834/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113834/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113834 Building REAL300020113835 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113835' /scratch/stefan/7770410/working/building/REAL300020113835 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113835 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113835/0 /scratch/stefan/7770410/working/building/REAL300020113835 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1282) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1282 `/scratch/stefan/7770410/working/3D/1282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=NNC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020113835.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113835 none CCOC1=NNC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 18, 11, 11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 46, 62, 79, 79, 79, 79, 11, 11, 1, 11, 35, 35, 35, 35, 35, 11, 6, 1, 1, 1, 1, 11, 46, 46, 62, 62, 1, 1, 11] 201 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45]) total number of confs: 393 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113835 none CCOC1=NNC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 74, 57, 57, 57, 57, 41, 41, 41, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 11, 57, 109, 109, 109, 109, 109, 57, 41, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 57] 201 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 384 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113835 none CCOC1=NNC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 57, 57, 57, 127, 169, 182, 182, 182, 182, 57, 57, 11, 1, 12, 12, 12, 12, 12, 1, 4, 11, 11, 11, 11, 57, 127, 127, 169, 169, 11, 11, 1] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 45, 26] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 711 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113835 none CCOC1=NNC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 192, 183, 183, 183, 183, 176, 176, 176, 77, 77, 77, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 77, 183, 201, 201, 201, 201, 201, 183, 176, 77, 77, 77, 77, 14, 6, 6, 4, 4, 77, 77, 183] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 575 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113835 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113835/1 /scratch/stefan/7770410/working/building/REAL300020113835 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1283) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1283 `/scratch/stefan/7770410/working/3D/1283' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=NNC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020113835.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113835 none CCOC1=NNC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 19, 12, 12, 12, 12, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 45, 61, 78, 78, 78, 78, 11, 11, 1, 12, 35, 35, 35, 35, 35, 12, 6, 1, 1, 1, 1, 11, 45, 45, 61, 61, 1, 1, 12] 201 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45]) total number of confs: 385 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113835 none CCOC1=NNC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 74, 58, 58, 58, 58, 41, 41, 41, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 11, 58, 110, 110, 110, 110, 110, 58, 41, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 58] 201 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 382 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113835 none CCOC1=NNC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 58, 58, 58, 126, 168, 183, 183, 183, 183, 58, 58, 12, 1, 12, 12, 12, 12, 12, 1, 4, 12, 12, 12, 12, 58, 126, 126, 168, 168, 12, 12, 1] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 45, 26] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 711 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113835 none CCOC1=NNC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 191, 183, 183, 183, 183, 176, 176, 176, 77, 77, 77, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 77, 183, 201, 201, 201, 201, 201, 183, 176, 77, 77, 77, 77, 14, 6, 6, 4, 4, 77, 77, 183] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 581 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113835 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113835 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113835/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113835/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113835 Building REAL300020113836 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113836' /scratch/stefan/7770410/working/building/REAL300020113836 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113836 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113836/0 /scratch/stefan/7770410/working/building/REAL300020113836 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1284) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1284 `/scratch/stefan/7770410/working/3D/1284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C(F)C=C1F) `REAL300020113836.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113836 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C(F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 53, 71, 87, 87, 87, 87, 12, 12, 1, 19, 19, 19, 9, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 12, 53, 53, 71, 71, 1, 1, 19] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 367 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113836 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C(F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 48, 48, 48, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 12, 100, 100, 100, 55, 100, 100, 100, 100, 100, 48, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 100] 201 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 415 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113836 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C(F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 8, 19, 19, 19, 100, 100, 100, 162, 201, 201, 201, 201, 201, 100, 100, 19, 1, 1, 1, 1, 1, 2, 2, 2, 1, 8, 19, 19, 19, 19, 100, 162, 162, 201, 201, 19, 19, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 44, 23, 24, 25, 26, 27, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 719 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113836 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C(F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 162, 162, 162, 88, 88, 88, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 88, 201, 201, 201, 201, 201, 201, 201, 201, 201, 162, 88, 88, 88, 88, 18, 6, 6, 4, 4, 88, 88, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 525 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113836 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113836/1 /scratch/stefan/7770410/working/building/REAL300020113836 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1285) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1285 `/scratch/stefan/7770410/working/3D/1285' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C(F)C=C1F) `REAL300020113836.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113836/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113836 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C(F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 53, 70, 86, 86, 86, 86, 12, 12, 1, 20, 20, 20, 9, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 12, 53, 53, 70, 70, 1, 1, 20] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 368 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113836 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C(F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 48, 48, 48, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 12, 100, 100, 100, 54, 100, 100, 100, 100, 100, 48, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 100] 201 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 414 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113836 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C(F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 8, 20, 20, 20, 100, 100, 100, 162, 201, 201, 201, 201, 201, 100, 100, 20, 1, 1, 1, 1, 1, 2, 2, 2, 1, 8, 20, 20, 20, 20, 100, 162, 162, 201, 201, 20, 20, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 44, 23, 24, 25, 26, 27, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 720 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113836 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C(F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 162, 162, 162, 87, 87, 87, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 87, 201, 201, 201, 201, 201, 201, 201, 201, 201, 162, 87, 87, 87, 87, 18, 6, 6, 4, 4, 87, 87, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 525 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113836 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113836 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113836/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113836/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113836 Building REAL300020113837 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113837' /scratch/stefan/7770410/working/building/REAL300020113837 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113837 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113837/0 /scratch/stefan/7770410/working/building/REAL300020113837 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1286) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1286 `/scratch/stefan/7770410/working/3D/1286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C(F)F)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113837.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113837 none CC1=NOC(C(F)F)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'F', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 15, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 23, 23, 23, 32, 32, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 30, 42, 42, 42, 42, 42, 10, 10, 1, 23, 23, 23, 32, 6, 1, 1, 1, 1, 10, 30, 30, 42, 42, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 42, 11, 12, 13, 14, 15, 43, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 255 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113837 none CC1=NOC(C(F)F)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'F', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 15, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 98, 98, 98, 121, 121, 30, 30, 30, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 10, 98, 98, 98, 121, 30, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10] 201 rigid atoms, others: [37, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 333 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113837 none CC1=NOC(C(F)F)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'F', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 15, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 9, 9, 9, 23, 23, 23, 98, 98, 98, 162, 201, 201, 201, 201, 201, 98, 98, 23, 2, 2, 2, 8, 9, 23, 23, 23, 23, 98, 162, 162, 201, 201, 23, 23] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 737 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113837 none CC1=NOC(C(F)F)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'F', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 15, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 88, 88, 88, 41, 41, 41, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 41, 201, 201, 201, 201, 88, 41, 41, 41, 41, 8, 4, 4, 2, 2, 41, 41] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 422 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113837 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113837/1 /scratch/stefan/7770410/working/building/REAL300020113837 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1287) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1287 `/scratch/stefan/7770410/working/3D/1287' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C(F)F)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113837.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113837 none CC1=NOC(C(F)F)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'F', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 15, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 23, 23, 23, 32, 32, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 30, 42, 42, 42, 42, 42, 10, 10, 1, 23, 23, 23, 32, 6, 1, 1, 1, 1, 10, 30, 30, 42, 42, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 42, 11, 12, 13, 14, 15, 43, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 255 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113837 none CC1=NOC(C(F)F)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'F', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 15, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 97, 97, 97, 97, 119, 119, 30, 30, 30, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 10, 97, 97, 97, 119, 30, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10] 201 rigid atoms, others: [37, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 326 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113837 none CC1=NOC(C(F)F)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'F', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 15, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 9, 9, 9, 23, 23, 23, 97, 97, 97, 162, 201, 201, 201, 201, 201, 97, 97, 23, 2, 2, 2, 8, 9, 23, 23, 23, 23, 97, 162, 162, 201, 201, 23, 23] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 745 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113837 none CC1=NOC(C(F)F)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'F', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 15, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 89, 89, 89, 42, 42, 42, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 42, 201, 201, 201, 201, 89, 42, 42, 42, 42, 8, 4, 4, 2, 2, 42, 42] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 421 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113837 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113837 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113837/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113837/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113837 Building REAL300020113838 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113838' /scratch/stefan/7770410/working/building/REAL300020113838 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113838 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113838/0 /scratch/stefan/7770410/working/building/REAL300020113838 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1288) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1288 `/scratch/stefan/7770410/working/3D/1288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(COCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NO1) `REAL300020113838.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113838 none CC1=CC(COCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 50, 25, 18, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 15, 25, 25, 25, 25, 25, 7, 7, 1, 82, 82, 82, 82, 82, 82, 50, 50, 18, 18, 5, 1, 1, 1, 1, 7, 15, 15, 25, 25, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 349 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113838 none CC1=CC(COCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [150, 150, 150, 121, 70, 59, 17, 17, 17, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 150, 150, 150, 150, 150, 150, 121, 121, 59, 59, 17, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 588 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113838 none CC1=CC(COCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 23, 35, 56, 56, 56, 82, 82, 82, 150, 150, 150, 182, 201, 201, 201, 201, 201, 150, 150, 82, 1, 1, 2, 2, 2, 1, 8, 8, 35, 35, 56, 82, 82, 82, 82, 150, 182, 182, 201, 201, 82, 82] 201 rigid atoms, others: [0, 1, 2, 3, 4, 26, 27, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 698 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113838 none CC1=CC(COCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 165, 93, 87, 28, 28, 28, 24, 24, 24, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 24, 201, 201, 201, 201, 201, 201, 165, 165, 87, 87, 28, 24, 24, 24, 24, 7, 4, 4, 2, 2, 24, 24] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 783 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113838 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113838/1 /scratch/stefan/7770410/working/building/REAL300020113838 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1289) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1289 `/scratch/stefan/7770410/working/3D/1289' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(COCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NO1) `REAL300020113838.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113838 none CC1=CC(COCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 50, 25, 18, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 15, 25, 25, 25, 25, 25, 7, 7, 1, 83, 83, 83, 83, 83, 83, 50, 50, 18, 18, 5, 1, 1, 1, 1, 7, 15, 15, 25, 25, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 351 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113838 none CC1=CC(COCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [150, 150, 150, 122, 70, 59, 17, 17, 17, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 150, 150, 150, 150, 150, 150, 122, 122, 59, 59, 17, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 590 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113838 none CC1=CC(COCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 23, 35, 56, 56, 56, 83, 83, 83, 150, 150, 150, 182, 201, 201, 201, 201, 201, 150, 150, 83, 1, 1, 2, 2, 2, 1, 8, 8, 35, 35, 56, 83, 83, 83, 83, 150, 182, 182, 201, 201, 83, 83] 201 rigid atoms, others: [0, 1, 2, 3, 4, 26, 27, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 700 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113838 none CC1=CC(COCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 167, 94, 88, 28, 28, 28, 24, 24, 24, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 24, 201, 201, 201, 201, 201, 201, 167, 167, 88, 88, 28, 24, 24, 24, 24, 7, 4, 4, 2, 2, 24, 24] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 792 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113838 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113838 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113838/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113838/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113838 Building REAL300020113839 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113839' /scratch/stefan/7770410/working/building/REAL300020113839 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113839 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113839/0 /scratch/stefan/7770410/working/building/REAL300020113839 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1290) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1290 `/scratch/stefan/7770410/working/3D/1290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(COCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020113839.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113839 none CC1=NOC(COCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 88, 51, 26, 18, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 16, 26, 26, 26, 26, 26, 7, 7, 1, 88, 88, 88, 88, 51, 51, 18, 18, 5, 1, 1, 1, 1, 7, 16, 16, 26, 26, 1, 1, 88] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47]) total number of confs: 363 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113839 none CC1=NOC(COCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 151, 151, 114, 65, 55, 16, 16, 16, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 151, 151, 151, 151, 114, 114, 55, 55, 16, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 151] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 570 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113839 none CC1=NOC(COCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 25, 39, 63, 63, 63, 88, 88, 88, 151, 151, 151, 184, 201, 201, 201, 201, 201, 151, 151, 88, 1, 2, 2, 2, 8, 8, 39, 39, 63, 88, 88, 88, 88, 151, 184, 184, 201, 201, 88, 88, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 47, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 699 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113839 none CC1=NOC(COCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 161, 90, 84, 29, 29, 29, 25, 25, 25, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 25, 201, 201, 201, 201, 161, 161, 84, 84, 29, 25, 25, 25, 25, 7, 4, 4, 2, 2, 25, 25, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 775 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113839 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113839/1 /scratch/stefan/7770410/working/building/REAL300020113839 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1291) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1291 `/scratch/stefan/7770410/working/3D/1291' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(COCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020113839.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113839 none CC1=NOC(COCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 88, 51, 26, 18, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 16, 26, 26, 26, 26, 26, 7, 7, 1, 88, 88, 88, 88, 51, 51, 18, 18, 5, 1, 1, 1, 1, 7, 16, 16, 26, 26, 1, 1, 88] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47]) total number of confs: 363 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113839 none CC1=NOC(COCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 151, 151, 114, 65, 55, 16, 16, 16, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 151, 151, 151, 151, 114, 114, 55, 55, 16, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 151] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 570 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113839 none CC1=NOC(COCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 25, 39, 63, 63, 63, 88, 88, 88, 151, 151, 151, 185, 201, 201, 201, 201, 201, 151, 151, 88, 1, 2, 2, 2, 8, 8, 39, 39, 63, 88, 88, 88, 88, 151, 185, 185, 201, 201, 88, 88, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 47, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 699 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113839 none CC1=NOC(COCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 163, 90, 85, 29, 29, 29, 25, 25, 25, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 25, 201, 201, 201, 201, 163, 163, 85, 85, 29, 25, 25, 25, 25, 7, 4, 4, 2, 2, 25, 25, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 782 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113839 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113839 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113839/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113839/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113839 Building REAL300020113840 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113840' /scratch/stefan/7770410/working/building/REAL300020113840 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113840 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113840/0 /scratch/stefan/7770410/working/building/REAL300020113840 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1292) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1292 `/scratch/stefan/7770410/working/3D/1292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC=C1COCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113840.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113840 none CN1N=CC=C1COCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 90, 90, 48, 22, 16, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 18, 28, 28, 28, 28, 28, 7, 7, 1, 90, 90, 90, 90, 90, 48, 48, 16, 16, 5, 1, 1, 1, 1, 7, 18, 18, 28, 28, 1, 1] 201 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 357 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113840 none CN1N=CC=C1COCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 158, 158, 158, 102, 61, 50, 16, 16, 16, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 158, 158, 158, 158, 158, 102, 102, 50, 50, 16, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 528 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113840 none CN1N=CC=C1COCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 25, 49, 68, 68, 68, 90, 90, 90, 158, 158, 158, 189, 201, 201, 201, 201, 201, 158, 158, 90, 2, 2, 2, 1, 1, 7, 7, 49, 49, 68, 90, 90, 90, 90, 158, 189, 189, 201, 201, 90, 90] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 679 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113840 none CN1N=CC=C1COCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 152, 108, 97, 36, 36, 36, 26, 26, 26, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 26, 201, 201, 201, 201, 201, 152, 152, 97, 97, 36, 26, 26, 26, 26, 7, 4, 4, 2, 2, 26, 26] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 708 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113840 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113840/1 /scratch/stefan/7770410/working/building/REAL300020113840 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1293) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1293 `/scratch/stefan/7770410/working/3D/1293' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC=C1COCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113840.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113840 none CN1N=CC=C1COCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 90, 90, 48, 22, 16, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 18, 28, 28, 28, 28, 28, 7, 7, 1, 90, 90, 90, 90, 90, 48, 48, 16, 16, 5, 1, 1, 1, 1, 7, 18, 18, 28, 28, 1, 1] 201 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 357 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113840 none CN1N=CC=C1COCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 158, 158, 158, 102, 62, 51, 16, 16, 16, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 158, 158, 158, 158, 158, 102, 102, 51, 51, 16, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 525 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113840 none CN1N=CC=C1COCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 25, 48, 67, 67, 67, 90, 90, 90, 158, 158, 158, 188, 201, 201, 201, 201, 201, 158, 158, 90, 2, 2, 2, 1, 1, 7, 7, 48, 48, 67, 90, 90, 90, 90, 158, 188, 188, 201, 201, 90, 90] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 680 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113840 none CN1N=CC=C1COCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 153, 109, 98, 37, 37, 37, 27, 27, 27, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 27, 201, 201, 201, 201, 201, 153, 153, 98, 98, 37, 27, 27, 27, 27, 8, 4, 4, 2, 2, 27, 27] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 708 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113840 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113840 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113840/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113840/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113840 Building REAL300020113841 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113841' /scratch/stefan/7770410/working/building/REAL300020113841 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for REAL300020113841 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113841/0 /scratch/stefan/7770410/working/building/REAL300020113841 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1294) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1294 `/scratch/stefan/7770410/working/3D/1294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2N=CNC2=N1) `REAL300020113841.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113841 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2N=CNC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 1, 1, 13, 57, 81, 81, 81, 81, 81, 81, 81, 81, 57, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13, 81, 81, 81, 81] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 228 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113841 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2N=CNC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 91, 91, 91, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 91, 200, 201, 201, 201, 201, 201, 201, 201, 201, 200, 91, 91, 91, 91, 13, 6, 6, 4, 4, 91, 91, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 549 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113841 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2N=CNC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 55, 78, 91, 91, 91, 91, 13, 13, 1, 6, 12, 12, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 13, 55, 55, 78, 78, 1, 1, 12, 12, 12, 12] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113841 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2N=CNC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 12, 12, 12, 81, 81, 81, 162, 201, 201, 201, 201, 201, 81, 81, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 12, 12, 12, 12, 81, 162, 162, 201, 201, 12, 12, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 754 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113841 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113841/1 /scratch/stefan/7770410/working/building/REAL300020113841 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1295) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1295 `/scratch/stefan/7770410/working/3D/1295' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2N=CNC2=N1) `REAL300020113841.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113841/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113841 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2N=CNC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 1, 1, 13, 57, 81, 81, 81, 81, 81, 81, 81, 81, 57, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13, 81, 81, 81, 81] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 228 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113841 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2N=CNC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 91, 91, 91, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 91, 200, 201, 201, 201, 201, 201, 201, 201, 201, 200, 91, 91, 91, 91, 13, 6, 6, 4, 4, 91, 91, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 549 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113841 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2N=CNC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 55, 78, 91, 91, 91, 91, 13, 13, 1, 6, 12, 12, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 13, 55, 55, 78, 78, 1, 1, 12, 12, 12, 12] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113841 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2N=CNC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 12, 12, 12, 81, 81, 81, 162, 201, 201, 201, 201, 201, 81, 81, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 12, 12, 12, 12, 81, 162, 162, 201, 201, 12, 12, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 754 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113841 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `2' /scratch/stefan/7770410/working/building/REAL300020113841/2 /scratch/stefan/7770410/working/building/REAL300020113841 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 2 (index: 1296) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1296 `/scratch/stefan/7770410/working/3D/1296' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2N=CN=C2N1) `REAL300020113841.mol2' -> `2.mol2' `temp.mol2' -> `REAL300020113841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113841/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113841 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2N=CN=C2N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 5, 5, 5, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 5, 7, 15, 15, 15, 15, 15, 15, 15, 15, 7, 5, 5, 5, 5, 1, 4, 4, 4, 4, 5, 5, 15, 15, 15, 15] 16 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 41 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113841 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2N=CN=C2N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 7, 7, 7, 5, 5, 5, 4, 2, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 16, 16, 16, 16, 16, 16, 16, 16, 8, 7, 7, 7, 7, 5, 4, 4, 2, 2, 7, 7, 16, 16, 16, 16] 16 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 40 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113841 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2N=CN=C2N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 6, 6, 6, 6, 6, 6, 5, 5, 1, 6, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 5, 6, 6, 6, 6, 1, 1, 15, 15, 15, 15] 16 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 36 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113841 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2N=CN=C2N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 8, 15, 15, 15, 15, 15, 15, 16, 16, 16, 16, 16, 16, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 15, 15, 15, 15, 15, 16, 16, 16, 16, 15, 15, 1, 1, 1, 1] 16 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 47 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113841 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `3' /scratch/stefan/7770410/working/building/REAL300020113841/3 /scratch/stefan/7770410/working/building/REAL300020113841 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 3 (index: 1297) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1297 `/scratch/stefan/7770410/working/3D/1297' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2N=CN=C2N1) `REAL300020113841.mol2' -> `3.mol2' `temp.mol2' -> `REAL300020113841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113841/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113841 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2N=CN=C2N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 5, 5, 5, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 5, 7, 15, 15, 15, 15, 15, 15, 15, 15, 7, 5, 5, 5, 5, 1, 4, 4, 4, 4, 5, 5, 15, 15, 15, 15] 16 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 41 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113841 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2N=CN=C2N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 7, 7, 7, 5, 5, 5, 4, 2, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 16, 16, 16, 16, 16, 16, 16, 16, 8, 7, 7, 7, 7, 5, 4, 4, 2, 2, 7, 7, 16, 16, 16, 16] 16 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 40 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113841 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2N=CN=C2N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 6, 6, 6, 6, 6, 6, 5, 5, 1, 6, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 5, 6, 6, 6, 6, 1, 1, 15, 15, 15, 15] 16 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 36 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113841 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2N=CN=C2N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 8, 15, 15, 15, 15, 15, 15, 16, 16, 16, 16, 16, 16, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 15, 15, 15, 15, 15, 16, 16, 16, 16, 15, 15, 1, 1, 1, 1] 16 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 47 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113841 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113841 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 2: /scratch/stefan/7770410/working/building/REAL300020113841/2.* 1: /scratch/stefan/7770410/working/building/REAL300020113841/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113841/0.* 3: /scratch/stefan/7770410/working/building/REAL300020113841/3.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113841 Building REAL300020113842 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113842' /scratch/stefan/7770410/working/building/REAL300020113842 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113842 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113842/0 /scratch/stefan/7770410/working/building/REAL300020113842 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1298) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1298 `/scratch/stefan/7770410/working/3D/1298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)NC(=O)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1) `REAL300020113842.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113842 none CC1=C(C)NC(=O)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 11, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 23, 36, 39, 39, 39, 39, 8, 8, 1, 28, 28, 28, 28, 28, 28, 28, 28, 5, 1, 1, 1, 1, 8, 23, 23, 36, 36, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 193 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113842 none CC1=C(C)NC(=O)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 11, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 105, 105, 105, 105, 24, 24, 24, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 8, 105, 105, 105, 105, 105, 105, 105, 105, 24, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 195 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113842 none CC1=C(C)NC(=O)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 11, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 28, 28, 28, 105, 105, 105, 161, 201, 201, 201, 201, 201, 105, 105, 28, 1, 2, 2, 2, 2, 2, 2, 1, 11, 28, 28, 28, 28, 105, 161, 161, 201, 201, 28, 28] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 742 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113842 none CC1=C(C)NC(=O)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 11, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 75, 75, 75, 40, 40, 40, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 40, 201, 201, 201, 201, 201, 201, 201, 201, 75, 40, 40, 40, 40, 10, 6, 6, 4, 4, 40, 40] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 401 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113842 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113842/1 /scratch/stefan/7770410/working/building/REAL300020113842 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1299) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1299 `/scratch/stefan/7770410/working/3D/1299' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)NC(=O)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1) `REAL300020113842.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113842 none CC1=C(C)NC(=O)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 11, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 23, 36, 39, 39, 39, 39, 8, 8, 1, 28, 28, 28, 28, 28, 28, 28, 28, 5, 1, 1, 1, 1, 8, 23, 23, 36, 36, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 193 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113842 none CC1=C(C)NC(=O)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 11, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 106, 106, 106, 106, 24, 24, 24, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 8, 106, 106, 106, 106, 106, 106, 106, 106, 24, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 196 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113842 none CC1=C(C)NC(=O)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 11, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 28, 28, 28, 106, 106, 106, 161, 201, 201, 201, 201, 201, 106, 106, 28, 1, 2, 2, 2, 2, 2, 2, 1, 11, 28, 28, 28, 28, 106, 161, 161, 201, 201, 28, 28] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 737 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113842 none CC1=C(C)NC(=O)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 11, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 75, 75, 75, 40, 40, 40, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 40, 201, 201, 201, 201, 201, 201, 201, 201, 75, 40, 40, 40, 40, 10, 6, 6, 4, 4, 40, 40] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 401 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113842 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113842 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113842/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113842/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113842 Building REAL300020113843 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113843' /scratch/stefan/7770410/working/building/REAL300020113843 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113843 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113843/0 /scratch/stefan/7770410/working/building/REAL300020113843 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1300) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1300 `/scratch/stefan/7770410/working/3D/1300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CC=CN2C=N1) `REAL300020113843.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113843 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CC=CN2C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 13, 59, 85, 85, 85, 85, 85, 85, 85, 85, 59, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13, 85, 85, 85, 85, 85] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 238 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113843 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CC=CN2C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 199, 102, 102, 102, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 102, 199, 201, 201, 201, 201, 201, 201, 201, 201, 199, 102, 102, 102, 102, 14, 6, 6, 4, 4, 102, 102, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 541 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113843 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CC=CN2C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 63, 86, 103, 103, 103, 103, 13, 13, 1, 6, 14, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 13, 63, 63, 86, 86, 1, 1, 14, 14, 14, 14, 14] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 397 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113843 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CC=CN2C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 14, 14, 14, 85, 85, 85, 171, 201, 201, 201, 201, 201, 85, 85, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 14, 14, 14, 14, 85, 171, 171, 201, 201, 14, 14, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 724 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113843 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113843/1 /scratch/stefan/7770410/working/building/REAL300020113843 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1301) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1301 `/scratch/stefan/7770410/working/3D/1301' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CC=CN2C=N1) `REAL300020113843.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113843 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CC=CN2C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 13, 59, 85, 85, 85, 85, 85, 85, 85, 85, 59, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13, 85, 85, 85, 85, 85] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 238 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113843 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CC=CN2C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 199, 102, 102, 102, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 102, 199, 201, 201, 201, 201, 201, 201, 201, 201, 199, 102, 102, 102, 102, 14, 6, 6, 4, 4, 102, 102, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 541 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113843 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CC=CN2C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 62, 85, 102, 102, 102, 102, 13, 13, 1, 6, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 13, 62, 62, 85, 85, 1, 1, 15, 15, 15, 15, 15] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 395 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113843 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CC=CN2C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 15, 15, 15, 85, 85, 85, 171, 201, 201, 201, 201, 201, 85, 85, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 15, 15, 15, 15, 85, 171, 171, 201, 201, 15, 15, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 724 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113843 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113843 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113843/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113843/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113843 Building REAL300020113844 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113844' /scratch/stefan/7770410/working/building/REAL300020113844 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113844 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113844/0 /scratch/stefan/7770410/working/building/REAL300020113844 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1302) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1302 `/scratch/stefan/7770410/working/3D/1302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C(C)S1) `REAL300020113844.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113844 none CC1=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 58, 78, 97, 97, 97, 97, 12, 12, 1, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 12, 58, 58, 78, 78, 1, 1, 19, 19, 19] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 39, 40, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43]) total number of confs: 372 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113844 none CC1=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 51, 51, 51, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 18, 18, 18, 18, 1, 1, 12, 96, 96, 96, 96, 96, 96, 51, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 96, 96, 96] 201 rigid atoms, others: [34, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 253 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113844 none CC1=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 19, 96, 96, 96, 158, 201, 201, 201, 201, 201, 96, 96, 19, 1, 1, 1, 2, 2, 2, 5, 19, 19, 19, 19, 96, 158, 158, 201, 201, 19, 19, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 735 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113844 none CC1=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 189, 189, 189, 98, 98, 98, 21, 21, 21, 6, 4, 1, 1, 1, 1, 1, 1, 21, 21, 98, 201, 201, 201, 201, 201, 201, 189, 98, 98, 98, 98, 21, 6, 6, 4, 4, 98, 98, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 547 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113844 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113844/1 /scratch/stefan/7770410/working/building/REAL300020113844 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1303) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1303 `/scratch/stefan/7770410/working/3D/1303' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C(C)S1) `REAL300020113844.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113844 none CC1=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 61, 80, 100, 100, 100, 100, 12, 12, 1, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 12, 61, 61, 80, 80, 1, 1, 18, 18, 18] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 39, 40, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43]) total number of confs: 376 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113844 none CC1=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 53, 53, 53, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 18, 18, 18, 18, 1, 1, 12, 95, 95, 95, 95, 95, 95, 53, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 95, 95, 95] 201 rigid atoms, others: [34, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 255 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113844 none CC1=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 95, 95, 95, 160, 201, 201, 201, 201, 201, 95, 95, 18, 1, 1, 1, 2, 2, 2, 5, 18, 18, 18, 18, 95, 160, 160, 201, 201, 18, 18, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 730 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113844 none CC1=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 191, 191, 191, 101, 101, 101, 23, 23, 23, 6, 4, 1, 1, 1, 1, 1, 1, 23, 23, 101, 201, 201, 201, 201, 201, 201, 191, 101, 101, 101, 101, 23, 6, 6, 4, 4, 101, 101, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 543 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113844 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113844 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113844/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113844/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113844 Building REAL300020113845 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113845' /scratch/stefan/7770410/working/building/REAL300020113845 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113845 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113845/0 /scratch/stefan/7770410/working/building/REAL300020113845 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1304) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1304 `/scratch/stefan/7770410/working/3D/1304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC1) `REAL300020113845.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113845 none CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 35, 35, 35, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 96, 104, 104, 104, 96, 96, 96, 96, 35, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 104, 104, 104, 104, 104, 104, 104] 201 rigid atoms, others: [34, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 399 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113845 none CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 118, 118, 118, 56, 56, 56, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 56, 201, 201, 201, 201, 201, 201, 201, 201, 118, 56, 56, 56, 56, 10, 6, 6, 4, 4, 56, 56, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 742 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113845 none CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 46, 56, 56, 56, 56, 11, 11, 1, 21, 28, 28, 28, 21, 21, 21, 21, 6, 1, 1, 1, 1, 11, 31, 31, 46, 46, 1, 1, 28, 28, 28, 28, 28, 28, 28] 201 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 39, 40, 20, 30, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113845 none CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 13, 13, 13, 28, 28, 28, 104, 104, 104, 168, 201, 201, 201, 201, 201, 104, 104, 28, 1, 1, 1, 1, 3, 3, 3, 3, 13, 28, 28, 28, 28, 104, 168, 168, 201, 201, 28, 28, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 47, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 708 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113845 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113845/1 /scratch/stefan/7770410/working/building/REAL300020113845 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1305) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1305 `/scratch/stefan/7770410/working/3D/1305' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC1) `REAL300020113845.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113845 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 35, 35, 35, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 96, 105, 105, 105, 96, 96, 96, 96, 35, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 105, 105, 105, 105, 105, 105, 105] 201 rigid atoms, others: [34, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 403 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113845 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 119, 119, 119, 58, 58, 58, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 58, 201, 201, 201, 201, 201, 201, 201, 201, 119, 58, 58, 58, 58, 11, 6, 6, 4, 4, 58, 58, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 738 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113845 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 46, 57, 57, 57, 57, 11, 11, 1, 21, 29, 29, 29, 21, 21, 21, 21, 6, 1, 1, 1, 1, 11, 31, 31, 46, 46, 1, 1, 29, 29, 29, 29, 29, 29, 29] 201 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 39, 40, 20, 30, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 306 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113845 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 13, 13, 13, 29, 29, 29, 105, 105, 105, 168, 201, 201, 201, 201, 201, 105, 105, 29, 1, 1, 1, 1, 3, 3, 3, 3, 13, 29, 29, 29, 29, 105, 168, 168, 201, 201, 29, 29, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 47, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 706 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113845 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113845 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113845/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113845/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113845 Building REAL300020113846 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113846' /scratch/stefan/7770410/working/building/REAL300020113846 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113846 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113846/0 /scratch/stefan/7770410/working/building/REAL300020113846 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1306) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1306 `/scratch/stefan/7770410/working/3D/1306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CC=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113846.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113846 none CCC1=CC=CC=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 21, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 22, 34, 34, 34, 34, 34, 7, 7, 1, 36, 36, 36, 36, 36, 36, 36, 36, 36, 21, 21, 5, 1, 1, 1, 1, 7, 22, 22, 34, 34, 1, 1] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 240 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113846 none CCC1=CC=CC=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 113, 113, 113, 113, 78, 16, 16, 16, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 113, 113, 113, 113, 113, 113, 113, 113, 113, 78, 78, 16, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 367 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113846 none CCC1=CC=CC=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 19, 19, 19, 36, 36, 36, 113, 113, 113, 168, 201, 201, 201, 201, 201, 113, 113, 36, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 19, 36, 36, 36, 36, 113, 168, 168, 201, 201, 36, 36] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 8, 7, 34, 35, 36] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 725 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113846 none CCC1=CC=CC=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 152, 54, 54, 54, 36, 36, 36, 9, 9, 9, 5, 2, 1, 1, 1, 1, 1, 1, 9, 9, 36, 201, 201, 201, 201, 201, 201, 201, 201, 201, 152, 152, 54, 36, 36, 36, 36, 9, 5, 5, 2, 2, 36, 36] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 673 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113846 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113846/1 /scratch/stefan/7770410/working/building/REAL300020113846 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1307) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1307 `/scratch/stefan/7770410/working/3D/1307' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CC=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113846.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113846 none CCC1=CC=CC=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 21, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 22, 34, 34, 34, 34, 34, 7, 7, 1, 36, 36, 36, 36, 36, 36, 36, 36, 36, 21, 21, 5, 1, 1, 1, 1, 7, 22, 22, 34, 34, 1, 1] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 240 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113846 none CCC1=CC=CC=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 113, 113, 113, 113, 78, 16, 16, 16, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 113, 113, 113, 113, 113, 113, 113, 113, 113, 78, 78, 16, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 367 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113846 none CCC1=CC=CC=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 19, 19, 19, 36, 36, 36, 113, 113, 113, 168, 201, 201, 201, 201, 201, 113, 113, 36, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 19, 36, 36, 36, 36, 113, 168, 168, 201, 201, 36, 36] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 8, 7, 34, 35, 36] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 725 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113846 none CCC1=CC=CC=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 152, 54, 54, 54, 36, 36, 36, 9, 9, 9, 5, 2, 1, 1, 1, 1, 1, 1, 9, 9, 36, 201, 201, 201, 201, 201, 201, 201, 201, 201, 152, 152, 54, 36, 36, 36, 36, 9, 5, 5, 2, 2, 36, 36] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 673 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113846 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113846 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113846/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113846/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113846 Building REAL300020113847 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113847' /scratch/stefan/7770410/working/building/REAL300020113847 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113847 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113847/0 /scratch/stefan/7770410/working/building/REAL300020113847 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1308) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1308 `/scratch/stefan/7770410/working/3D/1308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1C=CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113847.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113847 none O=C(CC1C=CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 21, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 8, 8, 8, 25, 38, 38, 38, 38, 38, 8, 8, 1, 21, 21, 33, 33, 33, 33, 33, 33, 33, 33, 33, 6, 1, 1, 1, 1, 8, 25, 25, 38, 38, 1, 1] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 274 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113847 none O=C(CC1C=CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 88, 109, 109, 109, 109, 109, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 88, 88, 109, 109, 109, 109, 109, 109, 109, 109, 109, 25, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 413 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113847 none O=C(CC1C=CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 4, 1, 1, 1, 1, 1, 1, 1, 19, 19, 33, 33, 33, 109, 109, 109, 163, 201, 201, 201, 201, 201, 109, 109, 33, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 33, 33, 33, 33, 109, 163, 163, 201, 201, 33, 33] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 716 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113847 none O=C(CC1C=CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 195, 201, 201, 201, 201, 201, 38, 38, 38, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 38, 195, 195, 201, 201, 201, 201, 201, 201, 201, 201, 201, 72, 38, 38, 38, 38, 8, 4, 4, 2, 2, 38, 38] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 737 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113847 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113847/1 /scratch/stefan/7770410/working/building/REAL300020113847 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1309) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1309 `/scratch/stefan/7770410/working/3D/1309' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1C=CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113847.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113847 none O=C(CC1C=CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 21, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 8, 8, 8, 25, 38, 38, 38, 38, 38, 8, 8, 1, 21, 21, 33, 33, 33, 33, 33, 33, 33, 33, 33, 6, 1, 1, 1, 1, 8, 25, 25, 38, 38, 1, 1] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 274 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113847 none O=C(CC1C=CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 88, 109, 109, 109, 109, 109, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 88, 88, 109, 109, 109, 109, 109, 109, 109, 109, 109, 25, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 413 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113847 none O=C(CC1C=CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 4, 1, 1, 1, 1, 1, 1, 1, 19, 19, 33, 33, 33, 109, 109, 109, 163, 201, 201, 201, 201, 201, 109, 109, 33, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 33, 33, 33, 33, 109, 163, 163, 201, 201, 33, 33] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 716 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113847 none O=C(CC1C=CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 195, 201, 201, 201, 201, 201, 38, 38, 38, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 38, 195, 195, 201, 201, 201, 201, 201, 201, 201, 201, 201, 72, 38, 38, 38, 38, 8, 4, 4, 2, 2, 38, 38] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 737 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113847 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113847 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113847/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113847/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113847 Building REAL300020113848 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113848' /scratch/stefan/7770410/working/building/REAL300020113848 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113848 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113848/0 /scratch/stefan/7770410/working/building/REAL300020113848 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1310) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1310 `/scratch/stefan/7770410/working/3D/1310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=C(F)C=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113848.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113848 none O=C(CC1=CC=C(F)C=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 15, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 9, 9, 9, 33, 47, 50, 50, 50, 50, 9, 9, 1, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 9, 33, 33, 47, 47, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 43, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 292 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113848 none O=C(CC1=CC=C(F)C=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 15, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 101, 101, 101, 101, 101, 101, 101, 9, 9, 9, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 9, 101, 101, 101, 101, 101, 30, 9, 9, 9, 9, 1, 8, 8, 10, 10, 9, 9] 201 rigid atoms, others: [37, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 391 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113848 none O=C(CC1=CC=C(F)C=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 15, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 29, 29, 29, 101, 101, 101, 168, 201, 201, 201, 201, 201, 101, 101, 29, 3, 3, 1, 1, 1, 9, 29, 29, 29, 29, 101, 168, 168, 201, 201, 29, 29] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 706 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113848 none O=C(CC1=CC=C(F)C=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 15, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 201, 201, 201, 201, 201, 201, 201, 50, 50, 50, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 50, 201, 201, 201, 201, 201, 103, 50, 50, 50, 50, 12, 6, 6, 4, 4, 50, 50] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 723 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113848 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113848/1 /scratch/stefan/7770410/working/building/REAL300020113848 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1311) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1311 `/scratch/stefan/7770410/working/3D/1311' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=C(F)C=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113848.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113848 none O=C(CC1=CC=C(F)C=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 15, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 9, 9, 9, 33, 47, 50, 50, 50, 50, 9, 9, 1, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 9, 33, 33, 47, 47, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 43, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 292 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113848 none O=C(CC1=CC=C(F)C=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 15, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 101, 101, 101, 101, 101, 101, 101, 9, 9, 9, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 9, 101, 101, 101, 101, 101, 30, 9, 9, 9, 9, 1, 8, 8, 10, 10, 9, 9] 201 rigid atoms, others: [37, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 391 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113848 none O=C(CC1=CC=C(F)C=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 15, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 29, 29, 29, 101, 101, 101, 169, 201, 201, 201, 201, 201, 101, 101, 29, 3, 3, 1, 1, 1, 9, 29, 29, 29, 29, 101, 169, 169, 201, 201, 29, 29] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 703 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113848 none O=C(CC1=CC=C(F)C=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 15, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 201, 201, 201, 201, 201, 201, 201, 50, 50, 50, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 50, 201, 201, 201, 201, 201, 103, 50, 50, 50, 50, 12, 6, 6, 4, 4, 50, 50] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 723 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113848 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113848 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113848/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113848/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113848 Building REAL300020113849 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113849' /scratch/stefan/7770410/working/building/REAL300020113849 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113849 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113849/0 /scratch/stefan/7770410/working/building/REAL300020113849 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1312) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1312 `/scratch/stefan/7770410/working/3D/1312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020113849.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113849 none CCC1=CC=CC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 22, 22, 22, 22, 22, 11, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 17, 27, 27, 27, 27, 27, 7, 7, 1, 18, 39, 39, 39, 39, 39, 22, 22, 22, 11, 11, 5, 1, 1, 1, 1, 7, 17, 17, 27, 27, 1, 1, 22] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50]) total number of confs: 283 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113849 none CCC1=CC=CC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 67, 67, 66, 67, 67, 36, 16, 16, 16, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 59, 124, 124, 124, 124, 124, 67, 67, 67, 36, 36, 16, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 67] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 590 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113849 none CCC1=CC=CC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 22, 22, 22, 67, 67, 67, 94, 111, 111, 111, 111, 111, 67, 67, 22, 1, 2, 2, 3, 2, 2, 1, 1, 1, 4, 4, 11, 22, 22, 22, 22, 67, 94, 94, 111, 111, 22, 22, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 7, 34, 50, 35, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 374 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113849 none CCC1=CC=CC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 112, 112, 111, 112, 112, 63, 38, 38, 38, 28, 28, 28, 8, 8, 8, 5, 2, 1, 1, 1, 1, 1, 1, 8, 8, 28, 103, 201, 201, 201, 201, 201, 112, 112, 112, 63, 63, 38, 28, 28, 28, 28, 8, 5, 5, 2, 2, 28, 28, 112] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 895 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113849 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113849/1 /scratch/stefan/7770410/working/building/REAL300020113849 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1313) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1313 `/scratch/stefan/7770410/working/3D/1313' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020113849.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113849/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113849 none CCC1=CC=CC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 23, 23, 23, 23, 23, 11, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 17, 27, 27, 27, 27, 27, 7, 7, 1, 19, 40, 40, 40, 40, 40, 23, 23, 23, 11, 11, 5, 1, 1, 1, 1, 7, 17, 17, 27, 27, 1, 1, 23] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50]) total number of confs: 284 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113849 none CCC1=CC=CC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 68, 68, 67, 68, 68, 36, 16, 16, 16, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 60, 125, 125, 125, 125, 125, 68, 68, 68, 36, 36, 16, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 68] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 592 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113849 none CCC1=CC=CC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 23, 23, 23, 68, 68, 68, 95, 112, 112, 112, 112, 112, 68, 68, 23, 1, 2, 2, 3, 2, 2, 1, 1, 1, 4, 4, 11, 23, 23, 23, 23, 68, 95, 95, 112, 112, 23, 23, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 7, 34, 50, 35, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 378 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113849 none CCC1=CC=CC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 112, 112, 110, 112, 112, 63, 38, 38, 38, 28, 28, 28, 8, 8, 8, 5, 2, 1, 1, 1, 1, 1, 1, 8, 8, 28, 103, 201, 201, 201, 201, 201, 112, 112, 112, 63, 63, 38, 28, 28, 28, 28, 8, 5, 5, 2, 2, 28, 28, 112] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 900 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113849 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113849 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113849/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113849/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113849 Building REAL300020113850 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113850' /scratch/stefan/7770410/working/building/REAL300020113850 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113850 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113850/0 /scratch/stefan/7770410/working/building/REAL300020113850 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1314) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1314 `/scratch/stefan/7770410/working/3D/1314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCN2C=NC=C2C1) `REAL300020113850.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113850 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCN2C=NC=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 8, 1, 8, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 10, 10, 10, 10, 1, 1, 11, 35, 108, 108, 108, 108, 108, 108, 108, 108, 35, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 108, 108, 108, 108, 108, 108, 108, 108, 108] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 312 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113850 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCN2C=NC=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 8, 1, 8, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 52, 52, 52, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 52, 105, 201, 201, 201, 201, 201, 201, 201, 201, 105, 52, 52, 52, 52, 10, 5, 5, 3, 3, 52, 52, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 584 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113850 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCN2C=NC=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 8, 1, 8, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 34, 49, 52, 52, 52, 52, 11, 11, 1, 6, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 34, 34, 49, 49, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113850 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCN2C=NC=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 8, 1, 8, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 22, 22, 22, 108, 108, 108, 172, 201, 201, 201, 201, 201, 108, 108, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 22, 22, 22, 22, 108, 172, 172, 201, 201, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 680 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113850 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113850/1 /scratch/stefan/7770410/working/building/REAL300020113850 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1315) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1315 `/scratch/stefan/7770410/working/3D/1315' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCN2C=NC=C2C1) `REAL300020113850.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113850/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113850 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCN2C=NC=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 8, 1, 8, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 10, 10, 10, 10, 1, 1, 11, 35, 108, 108, 108, 108, 108, 108, 108, 108, 35, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 108, 108, 108, 108, 108, 108, 108, 108, 108] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 312 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113850 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCN2C=NC=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 8, 1, 8, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 52, 52, 52, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 52, 105, 201, 201, 201, 201, 201, 201, 201, 201, 105, 52, 52, 52, 52, 10, 5, 5, 3, 3, 52, 52, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 584 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113850 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCN2C=NC=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 8, 1, 8, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 34, 49, 52, 52, 52, 52, 11, 11, 1, 6, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 34, 34, 49, 49, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113850 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCN2C=NC=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 8, 1, 8, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 22, 22, 22, 108, 108, 108, 172, 201, 201, 201, 201, 201, 108, 108, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 22, 22, 22, 22, 108, 172, 172, 201, 201, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 680 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113850 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113850 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113850/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113850/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113850 Building REAL300020113851 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113851' /scratch/stefan/7770410/working/building/REAL300020113851 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113851 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113851/0 /scratch/stefan/7770410/working/building/REAL300020113851 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1316) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1316 `/scratch/stefan/7770410/working/3D/1316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCC(F)(F)CC1) `REAL300020113851.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113851 none CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCC(F)(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 35, 49, 51, 51, 51, 51, 11, 11, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 11, 35, 35, 49, 49, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 41, 42, 20] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 234 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113851 none CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCC(F)(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 42, 42, 42, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 42, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 71, 71, 71, 71, 71, 71, 71, 71] 201 rigid atoms, others: [36, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 255 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113851 none CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCC(F)(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 2, 2, 2, 11, 11, 11, 71, 71, 71, 154, 201, 201, 201, 201, 201, 71, 71, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 11, 11, 11, 11, 71, 154, 154, 201, 201, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 43, 44, 45, 46, 47, 48, 49, 50, 21, 22, 23, 24, 25, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 775 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113851 none CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCC(F)(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 135, 135, 135, 52, 52, 52, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 52, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 135, 52, 52, 52, 52, 11, 6, 6, 4, 4, 52, 52, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 627 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113851 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113851/1 /scratch/stefan/7770410/working/building/REAL300020113851 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1317) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1317 `/scratch/stefan/7770410/working/3D/1317' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC(F)(F)CC1) `REAL300020113851.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113851/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113851 none CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC(F)(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 35, 49, 51, 51, 51, 51, 11, 11, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 11, 35, 35, 49, 49, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 41, 42, 20] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 234 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113851 none CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC(F)(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 42, 42, 42, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 42, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 71, 71, 71, 71, 71, 71, 71, 71] 201 rigid atoms, others: [36, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 255 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113851 none CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC(F)(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 2, 2, 2, 11, 11, 11, 71, 71, 71, 154, 201, 201, 201, 201, 201, 71, 71, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 11, 11, 11, 11, 71, 154, 154, 201, 201, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 43, 44, 45, 46, 47, 48, 49, 50, 21, 22, 23, 24, 25, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 769 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113851 none CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC(F)(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 134, 134, 134, 52, 52, 52, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 52, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 134, 52, 52, 52, 52, 11, 6, 6, 4, 4, 52, 52, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 627 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113851 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113851 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113851/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113851/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113851 Building REAL300020113852 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113852' /scratch/stefan/7770410/working/building/REAL300020113852 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113852 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113852/0 /scratch/stefan/7770410/working/building/REAL300020113852 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1318) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1318 `/scratch/stefan/7770410/working/3D/1318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1) `REAL300020113852.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113852 none CCOCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 40, 27, 18, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 33, 44, 44, 44, 44, 44, 12, 12, 1, 18, 18, 41, 41, 41, 41, 41, 27, 27, 6, 1, 1, 1, 1, 12, 33, 33, 44, 44, 1, 1, 18, 18, 18, 18] 201 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48]) total number of confs: 291 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113852 none CCOCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [126, 125, 102, 86, 49, 49, 49, 12, 12, 12, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 12, 86, 86, 126, 126, 126, 126, 126, 102, 102, 49, 12, 12, 12, 12, 1, 5, 5, 7, 7, 12, 12, 86, 86, 86, 86] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 413 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113852 none CCOCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 13, 6, 1, 1, 1, 5, 5, 5, 18, 18, 18, 86, 86, 86, 156, 195, 195, 195, 195, 195, 86, 86, 18, 1, 1, 14, 14, 14, 14, 14, 6, 6, 5, 18, 18, 18, 18, 86, 156, 156, 195, 195, 18, 18, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 45, 46, 47, 48, 24, 25] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 745 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113852 none CCOCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 198, 142, 142, 142, 45, 45, 45, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 45, 198, 198, 201, 201, 201, 201, 201, 201, 201, 142, 45, 45, 45, 45, 9, 4, 4, 2, 2, 45, 45, 198, 198, 198, 198] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 601 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113852 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113852/1 /scratch/stefan/7770410/working/building/REAL300020113852 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1319) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1319 `/scratch/stefan/7770410/working/3D/1319' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1) `REAL300020113852.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113852/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113852 none CCOCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 40, 27, 18, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 33, 44, 44, 44, 44, 44, 12, 12, 1, 18, 18, 41, 41, 41, 41, 41, 27, 27, 6, 1, 1, 1, 1, 12, 33, 33, 44, 44, 1, 1, 18, 18, 18, 18] 201 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48]) total number of confs: 291 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113852 none CCOCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [126, 125, 101, 86, 49, 49, 49, 12, 12, 12, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 12, 86, 86, 126, 126, 126, 126, 126, 101, 101, 49, 12, 12, 12, 12, 1, 5, 5, 7, 7, 12, 12, 86, 86, 86, 86] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 412 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113852 none CCOCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 13, 6, 1, 1, 1, 5, 5, 5, 18, 18, 18, 86, 86, 86, 156, 195, 195, 195, 195, 195, 86, 86, 18, 1, 1, 14, 14, 14, 14, 14, 6, 6, 5, 18, 18, 18, 18, 86, 156, 156, 195, 195, 18, 18, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 45, 46, 47, 48, 24, 25] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 748 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113852 none CCOCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 197, 140, 140, 140, 44, 44, 44, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 44, 197, 197, 201, 201, 201, 201, 201, 201, 201, 140, 44, 44, 44, 44, 8, 4, 4, 2, 2, 44, 44, 197, 197, 197, 197] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 608 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113852 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113852 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113852/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113852/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113852 Building REAL300020113853 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113853' /scratch/stefan/7770410/working/building/REAL300020113853 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113853 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113853/0 /scratch/stefan/7770410/working/building/REAL300020113853 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1320) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1320 `/scratch/stefan/7770410/working/3D/1320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C2=CC=CO2)ON=C1) `REAL300020113853.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113853 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C2=CC=CO2)ON=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 12, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 9, 9, 9, 1, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 1, 1, 9, 26, 87, 87, 120, 120, 120, 120, 87, 87, 87, 26, 9, 9, 9, 9, 1, 9, 9, 11, 11, 9, 9, 120, 120, 120, 87] 183 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 251 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113853 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C2=CC=CO2)ON=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 12, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [37, 10, 37, 37, 71, 71, 71, 120, 120, 120, 159, 183, 183, 183, 183, 183, 120, 120, 71, 9, 1, 1, 1, 1, 1, 1, 9, 9, 9, 37, 71, 71, 71, 71, 120, 159, 159, 183, 183, 71, 71, 1, 1, 1, 9] 183 rigid atoms, others: [41, 42, 43, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44]) total number of confs: 602 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113853 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C2=CC=CO2)ON=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 12, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 55, 55, 55, 18, 18, 18, 7, 4, 1, 1, 1, 1, 1, 1, 18, 18, 55, 119, 189, 189, 201, 201, 201, 201, 189, 189, 189, 119, 55, 55, 55, 55, 18, 7, 7, 4, 4, 55, 55, 201, 201, 201, 189] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 463 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113853 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C2=CC=CO2)ON=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 12, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 26, 36, 40, 40, 40, 40, 9, 9, 1, 6, 35, 35, 71, 71, 71, 71, 35, 35, 35, 6, 1, 1, 1, 1, 9, 26, 26, 36, 36, 1, 1, 71, 71, 71, 35] 183 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113853 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C2=CC=CO2)ON=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 12, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 35, 35, 35, 87, 87, 87, 131, 158, 160, 160, 160, 160, 87, 87, 35, 1, 1, 1, 9, 9, 9, 9, 1, 1, 1, 13, 35, 35, 35, 35, 87, 131, 131, 158, 158, 35, 35, 10, 9, 9, 1] 183 rigid atoms, others: [1, 44, 19, 20, 21, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 548 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113853 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113853/1 /scratch/stefan/7770410/working/building/REAL300020113853 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1321) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1321 `/scratch/stefan/7770410/working/3D/1321' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C2=CC=CO2)ON=C1) `REAL300020113853.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113853/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113853 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C2=CC=CO2)ON=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 12, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 9, 9, 9, 1, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 1, 1, 9, 27, 89, 89, 120, 120, 120, 120, 89, 89, 89, 27, 9, 9, 9, 9, 1, 9, 9, 11, 11, 9, 9, 120, 120, 120, 89] 183 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 250 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113853 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C2=CC=CO2)ON=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 12, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [36, 11, 36, 36, 71, 71, 71, 120, 120, 120, 159, 183, 183, 183, 183, 183, 120, 120, 71, 10, 1, 1, 1, 1, 1, 1, 10, 10, 10, 36, 71, 71, 71, 71, 120, 159, 159, 183, 183, 71, 71, 1, 1, 1, 10] 183 rigid atoms, others: [41, 42, 43, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44]) total number of confs: 602 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113853 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C2=CC=CO2)ON=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 12, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 56, 56, 56, 19, 19, 19, 7, 4, 1, 1, 1, 1, 1, 1, 19, 19, 56, 119, 189, 189, 201, 201, 201, 201, 189, 189, 189, 119, 56, 56, 56, 56, 19, 7, 7, 4, 4, 56, 56, 201, 201, 201, 189] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 460 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113853 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C2=CC=CO2)ON=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 12, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 26, 36, 41, 41, 41, 41, 9, 9, 1, 6, 35, 35, 71, 71, 71, 71, 35, 35, 35, 6, 1, 1, 1, 1, 9, 26, 26, 36, 36, 1, 1, 71, 71, 71, 35] 183 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113853 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C2=CC=CO2)ON=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 12, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 35, 35, 35, 89, 89, 89, 133, 160, 162, 162, 162, 162, 89, 89, 35, 1, 1, 1, 10, 10, 10, 10, 1, 1, 1, 13, 35, 35, 35, 35, 89, 133, 133, 160, 160, 35, 35, 11, 10, 10, 1] 183 rigid atoms, others: [1, 44, 19, 20, 21, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 552 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113853 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113853 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113853/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113853/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113853 Building REAL300020113854 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113854' /scratch/stefan/7770410/working/building/REAL300020113854 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113854 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113854/0 /scratch/stefan/7770410/working/building/REAL300020113854 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1322) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1322 `/scratch/stefan/7770410/working/3D/1322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C)=C1C(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113854.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113854 none CC1=NOC(C)=C1C(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 44, 44, 44, 31, 23, 31, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 27, 40, 40, 40, 40, 40, 11, 11, 1, 44, 44, 44, 44, 44, 44, 31, 31, 31, 31, 23, 23, 6, 1, 1, 1, 1, 11, 27, 27, 40, 40, 1, 1] 201 rigid atoms, others: [45, 44, 42, 43, 12, 13, 14, 15, 16, 51, 52, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50]) total number of confs: 302 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113854 none CC1=NOC(C)=C1C(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 128, 128, 128, 128, 105, 92, 105, 28, 28, 28, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 11, 128, 128, 128, 128, 128, 128, 105, 105, 105, 105, 92, 92, 28, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [46, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 465 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113854 none CC1=NOC(C)=C1C(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 23, 23, 23, 44, 44, 44, 128, 128, 128, 178, 201, 201, 201, 201, 201, 128, 128, 44, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 8, 8, 23, 44, 44, 44, 44, 128, 178, 178, 201, 201, 44, 44] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 683 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113854 none CC1=NOC(C)=C1C(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 180, 164, 180, 74, 74, 74, 38, 38, 38, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 38, 201, 201, 201, 201, 201, 201, 180, 180, 180, 180, 164, 164, 74, 38, 38, 38, 38, 9, 5, 5, 3, 3, 38, 38] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 754 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113854 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113854/1 /scratch/stefan/7770410/working/building/REAL300020113854 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1323) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1323 `/scratch/stefan/7770410/working/3D/1323' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C)=C1C(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113854.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113854 none CC1=NOC(C)=C1C(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 44, 44, 44, 31, 23, 31, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 27, 40, 41, 41, 41, 41, 11, 11, 1, 44, 44, 44, 44, 44, 44, 31, 31, 31, 31, 23, 23, 6, 1, 1, 1, 1, 11, 27, 27, 40, 40, 1, 1] 201 rigid atoms, others: [45, 44, 42, 43, 12, 13, 14, 15, 16, 51, 52, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50]) total number of confs: 304 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113854 none CC1=NOC(C)=C1C(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 128, 128, 128, 128, 105, 92, 105, 28, 28, 28, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 128, 128, 128, 128, 128, 128, 105, 105, 105, 105, 92, 92, 28, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [46, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 467 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113854 none CC1=NOC(C)=C1C(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 23, 23, 23, 44, 44, 44, 128, 128, 128, 178, 201, 201, 201, 201, 201, 128, 128, 44, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 8, 8, 23, 44, 44, 44, 44, 128, 178, 178, 201, 201, 44, 44] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 682 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113854 none CC1=NOC(C)=C1C(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 180, 164, 180, 74, 74, 74, 38, 38, 38, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 38, 201, 201, 201, 201, 201, 201, 180, 180, 180, 180, 164, 164, 74, 38, 38, 38, 38, 9, 5, 5, 3, 3, 38, 38] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 754 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113854 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113854 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113854/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113854/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113854 Building REAL300020113855 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113855' /scratch/stefan/7770410/working/building/REAL300020113855 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113855 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113855/0 /scratch/stefan/7770410/working/building/REAL300020113855 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1324) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1324 `/scratch/stefan/7770410/working/3D/1324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CC(F)(F)C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113855.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113855 none O=C(CC1CC(F)(F)C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 15, 15, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 20, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 35, 35, 35, 35, 8, 8, 1, 20, 20, 37, 37, 37, 37, 37, 5, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 274 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113855 none O=C(CC1CC(F)(F)C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 15, 15, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 65, 101, 101, 101, 101, 101, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 65, 65, 101, 101, 101, 101, 101, 24, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 402 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113855 none O=C(CC1CC(F)(F)C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 15, 15, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 5, 1, 1, 1, 1, 1, 1, 1, 18, 18, 37, 37, 37, 101, 101, 101, 153, 201, 201, 201, 201, 201, 101, 101, 37, 5, 5, 1, 1, 1, 1, 1, 18, 37, 37, 37, 37, 101, 153, 153, 201, 201, 37, 37] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 760 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113855 none O=C(CC1CC(F)(F)C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 15, 15, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 131, 201, 201, 201, 201, 201, 35, 35, 35, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 35, 131, 131, 201, 201, 201, 201, 201, 65, 35, 35, 35, 35, 7, 4, 4, 2, 2, 35, 35] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 809 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113855 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113855/1 /scratch/stefan/7770410/working/building/REAL300020113855 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1325) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1325 `/scratch/stefan/7770410/working/3D/1325' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CC(F)(F)C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113855.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113855/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113855 none O=C(CC1CC(F)(F)C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 15, 15, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 20, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 35, 35, 35, 35, 8, 8, 1, 20, 20, 37, 37, 37, 37, 37, 5, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 274 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113855 none O=C(CC1CC(F)(F)C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 15, 15, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 65, 101, 101, 101, 101, 101, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 65, 65, 101, 101, 101, 101, 101, 24, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 402 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113855 none O=C(CC1CC(F)(F)C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 15, 15, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 5, 1, 1, 1, 1, 1, 1, 1, 18, 18, 37, 37, 37, 101, 101, 101, 153, 201, 201, 201, 201, 201, 101, 101, 37, 5, 5, 1, 1, 1, 1, 1, 18, 37, 37, 37, 37, 101, 153, 153, 201, 201, 37, 37] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 760 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113855 none O=C(CC1CC(F)(F)C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 15, 15, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 131, 201, 201, 201, 201, 201, 35, 35, 35, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 35, 131, 131, 201, 201, 201, 201, 201, 64, 35, 35, 35, 35, 7, 4, 4, 2, 2, 35, 35] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 813 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113855 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113855 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113855/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113855/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113855 Building REAL300020113856 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113856' /scratch/stefan/7770410/working/building/REAL300020113856 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113856 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113856/0 /scratch/stefan/7770410/working/building/REAL300020113856 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1326) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1326 `/scratch/stefan/7770410/working/3D/1326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2=NNC(=O)N2C1) `REAL300020113856.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113856 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2=NNC(=O)N2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 33, 109, 109, 109, 109, 109, 109, 109, 109, 109, 33, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 109, 109, 109, 109, 109, 109, 109, 109] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 317 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113856 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2=NNC(=O)N2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 52, 52, 52, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 52, 108, 201, 201, 201, 201, 201, 201, 201, 201, 201, 108, 52, 52, 52, 52, 11, 6, 6, 4, 4, 52, 52, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 607 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113856 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2=NNC(=O)N2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 32, 46, 52, 52, 52, 52, 11, 11, 1, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 11, 32, 32, 46, 46, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113856 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2=NNC(=O)N2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 26, 26, 26, 109, 109, 109, 172, 201, 201, 201, 201, 201, 109, 109, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 26, 26, 26, 26, 109, 172, 172, 201, 201, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 672 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113856 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113856/1 /scratch/stefan/7770410/working/building/REAL300020113856 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1327) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1327 `/scratch/stefan/7770410/working/3D/1327' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2=NNC(=O)N2C1) `REAL300020113856.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113856 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2=NNC(=O)N2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 33, 109, 109, 109, 109, 109, 109, 109, 109, 109, 33, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 109, 109, 109, 109, 109, 109, 109, 109] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 317 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113856 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2=NNC(=O)N2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 51, 51, 51, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 51, 108, 201, 201, 201, 201, 201, 201, 201, 201, 201, 108, 51, 51, 51, 51, 10, 6, 6, 4, 4, 51, 51, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 613 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113856 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2=NNC(=O)N2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 45, 51, 51, 51, 51, 11, 11, 1, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 11, 31, 31, 45, 45, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113856 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2=NNC(=O)N2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 8, 8, 1, 11, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 26, 26, 26, 109, 109, 109, 173, 201, 201, 201, 201, 201, 109, 109, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 26, 26, 26, 26, 109, 173, 173, 201, 201, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 671 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113856 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113856 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113856/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113856/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113856 Building REAL300020113857 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113857' /scratch/stefan/7770410/working/building/REAL300020113857 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113857 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113857/0 /scratch/stefan/7770410/working/building/REAL300020113857 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1328) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1328 `/scratch/stefan/7770410/working/3D/1328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=NN(C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113857.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113857 none COCC1=NN(C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 52, 22, 22, 22, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 27, 35, 44, 44, 44, 44, 7, 7, 1, 81, 81, 81, 52, 52, 22, 22, 22, 22, 6, 1, 1, 1, 1, 7, 27, 27, 35, 35, 1, 1] 201 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 366 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113857 none COCC1=NN(C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 96, 47, 47, 47, 47, 47, 47, 21, 21, 21, 7, 7, 7, 1, 1, 1, 1, 1, 7, 9, 14, 14, 14, 14, 1, 1, 7, 128, 128, 128, 96, 96, 47, 47, 47, 47, 21, 7, 7, 7, 7, 1, 7, 7, 9, 9, 7, 7] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 424 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113857 none COCC1=NN(C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 22, 22, 22, 47, 47, 47, 103, 121, 135, 135, 135, 135, 47, 47, 22, 19, 19, 19, 7, 7, 2, 2, 2, 1, 9, 22, 22, 22, 22, 47, 103, 103, 121, 121, 22, 22] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 36] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 513 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113857 none COCC1=NN(C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 136, 136, 136, 136, 136, 136, 82, 82, 82, 51, 51, 51, 22, 22, 22, 6, 4, 1, 1, 1, 1, 1, 1, 22, 22, 51, 201, 201, 201, 201, 201, 136, 136, 136, 136, 82, 51, 51, 51, 51, 22, 6, 6, 4, 4, 51, 51] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 682 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113857 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113857/1 /scratch/stefan/7770410/working/building/REAL300020113857 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1329) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1329 `/scratch/stefan/7770410/working/3D/1329' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=NN(C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113857.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113857 none COCC1=NN(C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 52, 22, 22, 22, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 27, 35, 45, 45, 45, 45, 7, 7, 1, 81, 81, 81, 52, 52, 22, 22, 22, 22, 6, 1, 1, 1, 1, 7, 27, 27, 35, 35, 1, 1] 201 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 368 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113857 none COCC1=NN(C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 96, 47, 47, 47, 47, 47, 47, 21, 21, 21, 7, 7, 7, 1, 1, 1, 1, 1, 7, 9, 14, 14, 14, 14, 1, 1, 7, 127, 127, 127, 96, 96, 47, 47, 47, 47, 21, 7, 7, 7, 7, 1, 7, 7, 9, 9, 7, 7] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 422 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113857 none COCC1=NN(C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 22, 22, 22, 47, 47, 47, 103, 121, 135, 135, 135, 135, 47, 47, 22, 19, 19, 19, 7, 7, 2, 2, 2, 1, 9, 22, 22, 22, 22, 47, 103, 103, 121, 121, 22, 22] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 36] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 510 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113857 none COCC1=NN(C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 136, 136, 136, 136, 136, 136, 82, 82, 82, 52, 52, 52, 22, 22, 22, 6, 4, 1, 1, 1, 1, 1, 1, 22, 22, 52, 201, 201, 201, 201, 201, 136, 136, 136, 136, 82, 52, 52, 52, 52, 22, 6, 6, 4, 4, 52, 52] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 677 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113857 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113857 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113857/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113857/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113857 Building REAL300020113858 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113858' /scratch/stefan/7770410/working/building/REAL300020113858 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113858 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113858/0 /scratch/stefan/7770410/working/building/REAL300020113858 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1330) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1330 `/scratch/stefan/7770410/working/3D/1330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C2CCC2)=N1) `REAL300020113858.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113858 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C2CCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 44, 44, 44, 44, 44, 11, 11, 1, 15, 15, 29, 29, 29, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 11, 31, 31, 44, 44, 1, 1, 29, 29, 29, 29, 29, 29, 29] 201 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 43, 44, 22] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 243 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113858 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C2CCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 13, 13, 13, 29, 29, 29, 104, 104, 104, 161, 201, 201, 201, 201, 201, 104, 104, 29, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 13, 29, 29, 29, 29, 104, 161, 161, 201, 201, 29, 29, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 698 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113858 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C2CCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 29, 29, 29, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 11, 63, 63, 104, 104, 104, 63, 63, 63, 63, 63, 29, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 104, 104, 104, 104, 104, 104, 104] 201 rigid atoms, others: [38, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 309 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113858 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C2CCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 63, 63, 63, 120, 162, 162, 162, 162, 162, 63, 63, 15, 1, 1, 7, 7, 7, 1, 2, 2, 2, 1, 5, 15, 15, 15, 15, 63, 120, 120, 162, 162, 15, 15, 7, 7, 7, 7, 7, 7, 7] 201 rigid atoms, others: [0, 1, 2, 3, 4, 32, 23, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 637 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113858 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C2CCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 162, 84, 84, 84, 44, 44, 44, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 44, 162, 162, 201, 201, 201, 162, 162, 162, 162, 162, 84, 44, 44, 44, 44, 8, 4, 4, 2, 2, 44, 44, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 531 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113858 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113858/1 /scratch/stefan/7770410/working/building/REAL300020113858 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1331) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1331 `/scratch/stefan/7770410/working/3D/1331' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C2CCC2)=N1) `REAL300020113858.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113858 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C2CCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 44, 44, 44, 44, 44, 11, 11, 1, 15, 15, 29, 29, 29, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 11, 31, 31, 44, 44, 1, 1, 29, 29, 29, 29, 29, 29, 29] 201 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 43, 44, 22] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 243 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113858 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C2CCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 13, 13, 13, 29, 29, 29, 104, 104, 104, 161, 201, 201, 201, 201, 201, 104, 104, 29, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 13, 29, 29, 29, 29, 104, 161, 161, 201, 201, 29, 29, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 698 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113858 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C2CCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 29, 29, 29, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 11, 63, 63, 104, 104, 104, 63, 63, 63, 63, 63, 29, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 104, 104, 104, 104, 104, 104, 104] 201 rigid atoms, others: [38, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 309 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113858 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C2CCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 63, 63, 63, 120, 162, 162, 162, 162, 162, 63, 63, 15, 1, 1, 7, 7, 7, 1, 2, 2, 2, 1, 5, 15, 15, 15, 15, 63, 120, 120, 162, 162, 15, 15, 7, 7, 7, 7, 7, 7, 7] 201 rigid atoms, others: [0, 1, 2, 3, 4, 32, 23, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 637 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113858 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C2CCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 162, 85, 85, 85, 45, 45, 45, 9, 9, 9, 5, 2, 1, 1, 1, 1, 1, 1, 9, 9, 45, 162, 162, 201, 201, 201, 162, 162, 162, 162, 162, 85, 45, 45, 45, 45, 9, 5, 5, 2, 2, 45, 45, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 536 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113858 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113858 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113858/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113858/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113858 Building REAL300020113859 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113859' /scratch/stefan/7770410/working/building/REAL300020113859 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113859 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113859/0 /scratch/stefan/7770410/working/building/REAL300020113859 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1332) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1332 `/scratch/stefan/7770410/working/3D/1332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NN=C(C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113859.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113859 none CCC1=NN=C(C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [27, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 9, 10, 10, 10, 10, 10, 6, 6, 1, 27, 27, 27, 27, 27, 22, 22, 22, 22, 6, 1, 1, 1, 1, 6, 9, 9, 10, 10, 1, 1] 30 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 94 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113859 none CCC1=NN=C(C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [28, 25, 25, 25, 25, 25, 25, 25, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 6, 28, 28, 28, 28, 28, 25, 25, 25, 25, 13, 6, 6, 6, 6, 1, 5, 5, 7, 7, 6, 6] 30 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 96 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113859 none CCC1=NN=C(C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 22, 22, 22, 25, 25, 25, 30, 30, 30, 30, 30, 30, 25, 25, 22, 6, 6, 6, 6, 6, 2, 2, 2, 1, 8, 22, 22, 22, 22, 25, 30, 30, 30, 30, 22, 22] 30 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 36] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113859 none CCC1=NN=C(C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 30, 18, 18, 18, 11, 11, 11, 9, 9, 9, 6, 2, 1, 1, 1, 1, 1, 1, 9, 9, 11, 30, 30, 30, 30, 30, 30, 30, 30, 30, 18, 11, 11, 11, 11, 9, 6, 6, 2, 2, 11, 11] 30 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 77 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113859 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113859/1 /scratch/stefan/7770410/working/building/REAL300020113859 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1333) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1333 `/scratch/stefan/7770410/working/3D/1333' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NN=C(C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113859.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113859/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113859 none CCC1=NN=C(C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [26, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 9, 10, 10, 10, 10, 10, 6, 6, 1, 26, 26, 26, 26, 26, 22, 22, 22, 22, 6, 1, 1, 1, 1, 6, 9, 9, 10, 10, 1, 1] 29 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 88 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113859 none CCC1=NN=C(C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [27, 24, 24, 24, 24, 24, 24, 24, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 6, 27, 27, 27, 27, 27, 24, 24, 24, 24, 13, 6, 6, 6, 6, 1, 5, 5, 7, 7, 6, 6] 29 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 94 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113859 none CCC1=NN=C(C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 22, 22, 22, 24, 24, 24, 29, 29, 29, 29, 29, 29, 24, 24, 22, 6, 6, 6, 6, 6, 2, 2, 2, 1, 8, 22, 22, 22, 22, 24, 29, 29, 29, 29, 22, 22] 29 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 36] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 115 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113859 none CCC1=NN=C(C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 30, 18, 18, 18, 11, 11, 11, 9, 9, 9, 6, 2, 1, 1, 1, 1, 1, 1, 9, 9, 11, 30, 30, 30, 30, 30, 30, 30, 30, 30, 18, 11, 11, 11, 11, 9, 6, 6, 2, 2, 11, 11] 30 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 77 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113859 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113859 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113859/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113859/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113859 Building REAL300020113860 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113860' /scratch/stefan/7770410/working/building/REAL300020113860 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113860 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113860/0 /scratch/stefan/7770410/working/building/REAL300020113860 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1334) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1334 `/scratch/stefan/7770410/working/3D/1334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=NC2=CC=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=C21) `REAL300020113860.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113860 none CN1C=NC2=CC=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 35, 53, 63, 63, 63, 63, 12, 12, 1, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 12, 35, 35, 53, 53, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 272 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113860 none CN1C=NC2=CC=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 101, 101, 101, 101, 101, 46, 46, 46, 12, 12, 12, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 12, 101, 101, 101, 101, 101, 101, 101, 101, 46, 12, 12, 12, 12, 1, 6, 6, 8, 8, 12, 12] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 236 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113860 none CN1C=NC2=CC=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 21, 21, 21, 101, 101, 101, 163, 201, 201, 201, 201, 201, 101, 101, 21, 1, 2, 2, 2, 1, 1, 1, 1, 6, 21, 21, 21, 21, 101, 163, 163, 201, 201, 21, 21] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 34, 35, 33, 28] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 717 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113860 none CN1C=NC2=CC=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 142, 142, 142, 64, 64, 64, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 64, 201, 201, 201, 201, 201, 201, 201, 201, 142, 64, 64, 64, 64, 10, 6, 6, 4, 4, 64, 64] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 500 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113860 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113860/1 /scratch/stefan/7770410/working/building/REAL300020113860 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1335) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1335 `/scratch/stefan/7770410/working/3D/1335' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=NC2=CC=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=C21) `REAL300020113860.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113860/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113860 none CN1C=NC2=CC=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 36, 54, 64, 64, 64, 64, 12, 12, 1, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 12, 36, 36, 54, 54, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 275 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113860 none CN1C=NC2=CC=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 101, 101, 101, 101, 101, 46, 46, 46, 12, 12, 12, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 12, 101, 101, 101, 101, 101, 101, 101, 101, 46, 12, 12, 12, 12, 1, 6, 6, 8, 8, 12, 12] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 236 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113860 none CN1C=NC2=CC=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 21, 21, 21, 101, 101, 101, 163, 201, 201, 201, 201, 201, 101, 101, 21, 1, 2, 2, 2, 1, 1, 1, 1, 6, 21, 21, 21, 21, 101, 163, 163, 201, 201, 21, 21] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 34, 35, 33, 28] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 717 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113860 none CN1C=NC2=CC=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 142, 142, 142, 64, 64, 64, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 64, 201, 201, 201, 201, 201, 201, 201, 201, 142, 64, 64, 64, 64, 10, 6, 6, 4, 4, 64, 64] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 500 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113860 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113860 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113860/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113860/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113860 Building REAL300020113861 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113861' /scratch/stefan/7770410/working/building/REAL300020113861 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113861 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113861/0 /scratch/stefan/7770410/working/building/REAL300020113861 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1336) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1336 `/scratch/stefan/7770410/working/3D/1336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C)=C1C(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113861.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113861 none CC1=NNC(C)=C1C(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 23, 30, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 28, 41, 41, 41, 41, 41, 11, 11, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 23, 23, 6, 1, 1, 1, 1, 11, 28, 28, 41, 41, 1, 1] 201 rigid atoms, others: [45, 44, 43, 12, 13, 14, 15, 16, 52, 46, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 273 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113861 none CC1=NNC(C)=C1C(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 106, 106, 106, 106, 91, 106, 29, 29, 29, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 11, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 91, 91, 29, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [15, 47, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 430 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113861 none CC1=NNC(C)=C1C(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 16, 16, 16, 35, 35, 35, 109, 109, 109, 163, 201, 201, 201, 201, 201, 109, 109, 35, 2, 2, 2, 1, 2, 2, 2, 3, 3, 3, 3, 5, 5, 16, 35, 35, 35, 35, 109, 163, 163, 201, 201, 35, 35] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 734 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113861 none CC1=NNC(C)=C1C(C)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 182, 201, 85, 85, 85, 43, 43, 43, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 43, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 182, 182, 85, 43, 43, 43, 43, 10, 5, 5, 3, 3, 43, 43] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 796 number of broken/clashed sets: 201 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113861 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113861/1 /scratch/stefan/7770410/working/building/REAL300020113861 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1337) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1337 `/scratch/stefan/7770410/working/3D/1337' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C)=C1C(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113861.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113861 none CC1=NNC(C)=C1C(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 23, 30, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 28, 41, 42, 42, 42, 42, 11, 11, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 23, 23, 6, 1, 1, 1, 1, 11, 28, 28, 41, 41, 1, 1] 201 rigid atoms, others: [45, 44, 43, 12, 13, 14, 15, 16, 52, 46, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 275 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113861 none CC1=NNC(C)=C1C(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 106, 106, 106, 106, 92, 106, 29, 29, 29, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 92, 92, 29, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [15, 47, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 429 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113861 none CC1=NNC(C)=C1C(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 16, 16, 16, 35, 35, 35, 109, 109, 109, 163, 201, 201, 201, 201, 201, 109, 109, 35, 2, 2, 2, 1, 2, 2, 2, 3, 3, 3, 3, 5, 5, 16, 35, 35, 35, 35, 109, 163, 163, 201, 201, 35, 35] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 733 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113861 none CC1=NNC(C)=C1C(C)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 183, 201, 86, 86, 86, 43, 43, 43, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 43, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 183, 183, 86, 43, 43, 43, 43, 10, 5, 5, 3, 3, 43, 43] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 794 number of broken/clashed sets: 201 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113861 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113861 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113861/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113861/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113861 Building REAL300020113862 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113862' /scratch/stefan/7770410/working/building/REAL300020113862 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113862 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113862/0 /scratch/stefan/7770410/working/building/REAL300020113862 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1338) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1338 `/scratch/stefan/7770410/working/3D/1338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2C=CC1O2) `REAL300020113862.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113862 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2C=CC1O2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 12, 12, 12, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 12, 47, 96, 96, 96, 96, 96, 96, 47, 12, 12, 12, 12, 1, 8, 8, 10, 10, 12, 12, 96, 96, 96, 96, 96, 96, 96] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 325 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113862 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2C=CC1O2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 75, 75, 75, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 75, 165, 201, 201, 201, 201, 201, 201, 165, 75, 75, 75, 75, 13, 6, 6, 4, 4, 75, 75, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 596 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113862 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2C=CC1O2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 39, 59, 75, 75, 75, 75, 12, 12, 1, 6, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 12, 39, 39, 59, 59, 1, 1, 19, 19, 19, 19, 19, 19, 19] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 324 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113862 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2C=CC1O2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 19, 19, 19, 96, 96, 96, 175, 201, 201, 201, 201, 201, 96, 96, 19, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 19, 96, 175, 175, 201, 201, 19, 19, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 38, 39, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 672 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113862 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113862/1 /scratch/stefan/7770410/working/building/REAL300020113862 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1339) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1339 `/scratch/stefan/7770410/working/3D/1339' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2C=CC1O2) `REAL300020113862.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113862/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113862 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2C=CC1O2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 12, 12, 12, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 12, 47, 96, 96, 96, 96, 96, 96, 47, 12, 12, 12, 12, 1, 8, 8, 10, 10, 12, 12, 96, 96, 96, 96, 96, 96, 96] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 325 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113862 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2C=CC1O2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 75, 75, 75, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 75, 165, 201, 201, 201, 201, 201, 201, 165, 75, 75, 75, 75, 13, 6, 6, 4, 4, 75, 75, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 596 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113862 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2C=CC1O2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 39, 59, 75, 75, 75, 75, 12, 12, 1, 6, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 12, 39, 39, 59, 59, 1, 1, 19, 19, 19, 19, 19, 19, 19] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 324 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113862 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2C=CC1O2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 19, 19, 19, 96, 96, 96, 175, 201, 201, 201, 201, 201, 96, 96, 19, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 19, 96, 175, 175, 201, 201, 19, 19, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 38, 39, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 672 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113862 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113862 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113862/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113862/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113862 Building REAL300020113863 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113863' /scratch/stefan/7770410/working/building/REAL300020113863 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113863 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113863/0 /scratch/stefan/7770410/working/building/REAL300020113863 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1340) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1340 `/scratch/stefan/7770410/working/3D/1340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(C)(F)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113863.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113863 none CCCCC(C)(F)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 61, 34, 61, 61, 34, 34, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 101, 101, 101, 101, 101, 101, 101, 101, 101, 61, 61, 61, 34, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11] 201 rigid atoms, others: [43, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 458 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113863 none CCCCC(C)(F)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 168, 122, 168, 168, 122, 122, 63, 63, 63, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 63, 201, 201, 201, 201, 201, 201, 201, 201, 201, 168, 168, 168, 122, 63, 63, 63, 63, 11, 6, 6, 4, 4, 63, 63] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 793 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113863 none CCCCC(C)(F)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 37, 53, 63, 63, 63, 63, 11, 11, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 12, 12, 12, 6, 1, 1, 1, 1, 11, 37, 37, 53, 53, 1, 1] 201 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 48, 49, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113863 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113863/1 /scratch/stefan/7770410/working/building/REAL300020113863 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1341) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1341 `/scratch/stefan/7770410/working/3D/1341' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(C)(F)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113863.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113863/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113863 none CCCCC(C)(F)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 61, 34, 61, 61, 34, 34, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 101, 101, 101, 101, 101, 101, 101, 101, 101, 61, 61, 61, 34, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11] 201 rigid atoms, others: [43, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 458 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113863 none CCCCC(C)(F)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 168, 122, 168, 168, 122, 122, 63, 63, 63, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 63, 201, 201, 201, 201, 201, 201, 201, 201, 201, 168, 168, 168, 122, 63, 63, 63, 63, 11, 6, 6, 4, 4, 63, 63] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 793 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113863 none CCCCC(C)(F)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 37, 53, 63, 63, 63, 63, 11, 11, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 12, 12, 12, 6, 1, 1, 1, 1, 11, 37, 37, 53, 53, 1, 1] 201 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 48, 49, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113863 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113863 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113863/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113863/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113863 Building REAL300020113864 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113864' /scratch/stefan/7770410/working/building/REAL300020113864 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113864 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113864/0 /scratch/stefan/7770410/working/building/REAL300020113864 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1342) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1342 `/scratch/stefan/7770410/working/3D/1342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2=NC=CN2C1) `REAL300020113864.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113864 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2=NC=CN2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 8, 1, 1, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 34, 105, 105, 105, 105, 105, 105, 105, 105, 34, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 105, 105, 105, 105, 105, 105, 105, 105, 105] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 301 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113864 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2=NC=CN2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 8, 1, 1, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 53, 53, 53, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 53, 103, 201, 201, 201, 201, 201, 201, 201, 201, 103, 53, 53, 53, 53, 10, 6, 6, 4, 4, 53, 53, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 607 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113864 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2=NC=CN2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 8, 1, 1, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 30, 45, 52, 52, 52, 52, 11, 11, 1, 6, 23, 23, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 11, 30, 30, 45, 45, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113864 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2=NC=CN2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 8, 1, 1, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 23, 23, 23, 105, 105, 105, 162, 201, 201, 201, 201, 201, 105, 105, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 23, 23, 23, 23, 105, 162, 162, 201, 201, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 707 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113864 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113864/1 /scratch/stefan/7770410/working/building/REAL300020113864 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1343) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1343 `/scratch/stefan/7770410/working/3D/1343' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2=NC=CN2C1) `REAL300020113864.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113864 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2=NC=CN2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 8, 1, 1, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 34, 105, 105, 105, 105, 105, 105, 105, 105, 34, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 105, 105, 105, 105, 105, 105, 105, 105, 105] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 301 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113864 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2=NC=CN2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 8, 1, 1, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 52, 52, 52, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 52, 103, 201, 201, 201, 201, 201, 201, 201, 201, 103, 52, 52, 52, 52, 10, 6, 6, 4, 4, 52, 52, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 607 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113864 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2=NC=CN2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 8, 1, 1, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 30, 45, 52, 52, 52, 52, 11, 11, 1, 6, 23, 23, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 11, 30, 30, 45, 45, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113864 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2=NC=CN2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 8, 1, 1, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 23, 23, 23, 105, 105, 105, 162, 201, 201, 201, 201, 201, 105, 105, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 23, 23, 23, 23, 105, 162, 162, 201, 201, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 707 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113864 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113864 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113864/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113864/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113864 Building REAL300020113865 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113865' /scratch/stefan/7770410/working/building/REAL300020113865 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113865 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113865/0 /scratch/stefan/7770410/working/building/REAL300020113865 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1344) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1344 `/scratch/stefan/7770410/working/3D/1344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCN2C=CN=C2C1) `REAL300020113865.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113865 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCN2C=CN=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 8, 1, 1, 8, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 35, 98, 98, 98, 98, 98, 98, 98, 98, 35, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 98, 98, 98, 98, 98, 98, 98, 98, 98] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 291 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113865 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCN2C=CN=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 8, 1, 1, 8, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 57, 57, 57, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 57, 109, 201, 201, 201, 201, 201, 201, 201, 201, 109, 57, 57, 57, 57, 11, 6, 6, 4, 4, 57, 57, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 581 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113865 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCN2C=CN=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 8, 1, 1, 8, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 34, 50, 56, 56, 56, 56, 11, 11, 1, 6, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 34, 34, 50, 50, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113865 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCN2C=CN=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 8, 1, 1, 8, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 9, 22, 22, 22, 98, 98, 98, 158, 201, 201, 201, 201, 201, 98, 98, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 22, 22, 22, 22, 98, 158, 158, 201, 201, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 735 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113865 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113865/1 /scratch/stefan/7770410/working/building/REAL300020113865 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1345) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1345 `/scratch/stefan/7770410/working/3D/1345' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCN2C=CN=C2C1) `REAL300020113865.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113865 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCN2C=CN=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 8, 1, 1, 8, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 35, 98, 98, 98, 98, 98, 98, 98, 98, 35, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 98, 98, 98, 98, 98, 98, 98, 98, 98] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 291 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113865 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCN2C=CN=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 8, 1, 1, 8, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 56, 56, 56, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 56, 108, 201, 201, 201, 201, 201, 201, 201, 201, 108, 56, 56, 56, 56, 10, 6, 6, 4, 4, 56, 56, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 581 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113865 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCN2C=CN=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 8, 1, 1, 8, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 34, 50, 56, 56, 56, 56, 11, 11, 1, 6, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 34, 34, 50, 50, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113865 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCN2C=CN=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 8, 1, 1, 8, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 9, 22, 22, 22, 98, 98, 98, 158, 201, 201, 201, 201, 201, 98, 98, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 22, 22, 22, 22, 98, 158, 158, 201, 201, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 735 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113865 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113865 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113865/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113865/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113865 Building REAL300020113866 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113866' /scratch/stefan/7770410/working/building/REAL300020113866 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113866 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113866/0 /scratch/stefan/7770410/working/building/REAL300020113866 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1346) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1346 `/scratch/stefan/7770410/working/3D/1346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1OCCO[C@@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113866.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113866 none C[C@@H]1OCCO[C@@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 6, 12, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 44, 63, 76, 76, 76, 76, 13, 13, 1, 12, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 13, 44, 44, 63, 63, 1, 1] 201 rigid atoms, others: [45, 36, 37, 38, 39, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 311 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113866 none C[C@@H]1OCCO[C@@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 79, 79, 79, 79, 45, 79, 45, 45, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 13, 79, 79, 79, 79, 79, 79, 79, 45, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13] 201 rigid atoms, others: [40, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 283 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113866 none C[C@@H]1OCCO[C@@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 79, 79, 79, 166, 201, 201, 201, 201, 201, 79, 79, 12, 2, 2, 2, 1, 1, 1, 1, 4, 12, 12, 12, 12, 79, 166, 166, 201, 201, 12, 12] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 32, 33, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 737 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113866 none C[C@@H]1OCCO[C@@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 157, 201, 157, 157, 76, 76, 76, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 76, 201, 201, 201, 201, 201, 201, 201, 157, 76, 76, 76, 76, 12, 6, 6, 4, 4, 76, 76] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 608 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113866 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113866/1 /scratch/stefan/7770410/working/building/REAL300020113866 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1347) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1347 `/scratch/stefan/7770410/working/3D/1347' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1OCCO[C@@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113866.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113866/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113866 none C[C@@H]1OCCO[C@@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 6, 12, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 44, 63, 76, 76, 76, 76, 13, 13, 1, 12, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 13, 44, 44, 63, 63, 1, 1] 201 rigid atoms, others: [45, 36, 37, 38, 39, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 311 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113866 none C[C@@H]1OCCO[C@@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 79, 79, 79, 79, 45, 79, 45, 45, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 13, 79, 79, 79, 79, 79, 79, 79, 45, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13] 201 rigid atoms, others: [40, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 283 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113866 none C[C@@H]1OCCO[C@@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 79, 79, 79, 166, 201, 201, 201, 201, 201, 79, 79, 12, 2, 2, 2, 1, 1, 1, 1, 4, 12, 12, 12, 12, 79, 166, 166, 201, 201, 12, 12] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 32, 33, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 740 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113866 none C[C@@H]1OCCO[C@@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 157, 201, 157, 157, 76, 76, 76, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 76, 201, 201, 201, 201, 201, 201, 201, 157, 76, 76, 76, 76, 12, 6, 6, 4, 4, 76, 76] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 608 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113866 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113866 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113866/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113866/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113866 Building REAL300020113867 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113867' /scratch/stefan/7770410/working/building/REAL300020113867 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113867 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113867/0 /scratch/stefan/7770410/working/building/REAL300020113867 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1348) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1348 `/scratch/stefan/7770410/working/3D/1348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC1=O) `REAL300020113867.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113867 none CN1C=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 18, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 61, 82, 106, 106, 106, 106, 13, 13, 1, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 13, 61, 61, 82, 82, 1, 1, 19] 201 rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43]) total number of confs: 396 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113867 none CN1C=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 94, 51, 51, 51, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 21, 21, 21, 21, 1, 1, 13, 94, 94, 94, 94, 94, 94, 94, 51, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 94] 201 rigid atoms, others: [36, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 262 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113867 none CN1C=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 19, 94, 94, 94, 166, 201, 201, 201, 201, 201, 94, 94, 19, 1, 1, 1, 2, 2, 2, 1, 5, 19, 19, 19, 19, 94, 166, 166, 201, 201, 19, 19, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 24, 25, 26, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 687 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113867 none CN1C=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 186, 186, 186, 110, 110, 110, 23, 23, 23, 6, 4, 1, 1, 1, 1, 1, 1, 23, 23, 110, 201, 201, 201, 201, 201, 201, 201, 186, 110, 110, 110, 110, 23, 6, 6, 4, 4, 110, 110, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 534 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113867 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113867/1 /scratch/stefan/7770410/working/building/REAL300020113867 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1349) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1349 `/scratch/stefan/7770410/working/3D/1349' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC1=O) `REAL300020113867.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113867/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113867 none CN1C=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 18, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 61, 82, 106, 106, 106, 106, 13, 13, 1, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 13, 61, 61, 82, 82, 1, 1, 19] 201 rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43]) total number of confs: 396 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113867 none CN1C=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 94, 51, 51, 51, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 21, 21, 21, 21, 1, 1, 13, 94, 94, 94, 94, 94, 94, 94, 51, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 94] 201 rigid atoms, others: [36, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 262 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113867 none CN1C=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 19, 94, 94, 94, 166, 201, 201, 201, 201, 201, 94, 94, 19, 1, 1, 1, 2, 2, 2, 1, 5, 19, 19, 19, 19, 94, 166, 166, 201, 201, 19, 19, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 24, 25, 26, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 687 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113867 none CN1C=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 186, 186, 186, 110, 110, 110, 23, 23, 23, 6, 4, 1, 1, 1, 1, 1, 1, 23, 23, 110, 201, 201, 201, 201, 201, 201, 201, 186, 110, 110, 110, 110, 23, 6, 6, 4, 4, 110, 110, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 534 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113867 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113867 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113867/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113867/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113867 Building REAL300020113868 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113868' /scratch/stefan/7770410/working/building/REAL300020113868 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113868 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113868/0 /scratch/stefan/7770410/working/building/REAL300020113868 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1350) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1350 `/scratch/stefan/7770410/working/3D/1350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CNC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1) `REAL300020113868.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113868 none CCC1=CNC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 16, 16, 16, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 21, 33, 33, 33, 33, 33, 8, 8, 1, 16, 36, 36, 36, 36, 36, 16, 16, 16, 16, 5, 1, 1, 1, 1, 8, 21, 21, 33, 33, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 292 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113868 none CCC1=CNC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 57, 57, 57, 57, 57, 21, 21, 21, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 57, 102, 102, 102, 102, 102, 57, 57, 57, 57, 21, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 484 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113868 none CCC1=CNC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 16, 16, 16, 57, 57, 57, 100, 124, 124, 124, 124, 124, 57, 57, 16, 1, 6, 6, 6, 6, 6, 1, 1, 5, 5, 7, 16, 16, 16, 16, 57, 100, 100, 124, 124, 16, 16] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 496 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113868 none CCC1=CNC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 123, 123, 123, 123, 123, 56, 56, 56, 32, 32, 32, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 32, 123, 201, 201, 201, 201, 201, 123, 123, 123, 123, 56, 32, 32, 32, 32, 8, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 946 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113868 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113868/1 /scratch/stefan/7770410/working/building/REAL300020113868 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1351) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1351 `/scratch/stefan/7770410/working/3D/1351' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CNC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1) `REAL300020113868.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113868/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113868 none CCC1=CNC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 16, 16, 16, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 21, 33, 33, 33, 33, 33, 8, 8, 1, 16, 37, 37, 37, 37, 37, 16, 16, 16, 16, 5, 1, 1, 1, 1, 8, 21, 21, 33, 33, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 298 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113868 none CCC1=CNC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 56, 56, 56, 56, 56, 21, 21, 21, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 56, 102, 102, 102, 102, 102, 56, 56, 56, 56, 21, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 487 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113868 none CCC1=CNC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 16, 16, 16, 56, 56, 56, 99, 124, 124, 124, 124, 124, 56, 56, 16, 1, 6, 6, 6, 6, 6, 1, 1, 5, 5, 7, 16, 16, 16, 16, 56, 99, 99, 124, 124, 16, 16] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 501 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113868 none CCC1=CNC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 124, 124, 124, 124, 124, 58, 58, 58, 33, 33, 33, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 33, 124, 201, 201, 201, 201, 201, 124, 124, 124, 124, 58, 33, 33, 33, 33, 9, 4, 4, 2, 2, 33, 33] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 938 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113868 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113868 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113868/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113868/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113868 Building REAL300020113869 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113869' /scratch/stefan/7770410/working/building/REAL300020113869 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113869 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113869/0 /scratch/stefan/7770410/working/building/REAL300020113869 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1352) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1352 `/scratch/stefan/7770410/working/3D/1352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@H]1CC[C@H](C2CCC2)CC1) `REAL300020113869.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113869 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@H]1CC[C@H](C2CCC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 13, 48, 141, 141, 141, 141, 141, 141, 144, 144, 144, 141, 141, 48, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 141, 141, 141, 141, 144, 144, 144, 144, 144, 144, 144, 141, 141, 141, 141] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 432 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113869 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@H]1CC[C@H](C2CCC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 2, 16, 16, 37, 37, 37, 144, 144, 144, 175, 201, 201, 201, 201, 201, 144, 144, 37, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 2, 2, 16, 37, 37, 37, 37, 144, 175, 175, 201, 201, 37, 37, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2] 201 rigid atoms, others: [47, 48, 49, 50, 51, 52, 53, 23, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 54, 55, 56, 57]) total number of confs: 562 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113869 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@H]1CC[C@H](C2CCC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 39, 39, 39, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 39, 98, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 98, 39, 39, 39, 39, 8, 4, 4, 2, 2, 39, 39, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 607 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113869 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@H]1CC[C@H](C2CCC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 28, 37, 37, 37, 37, 37, 13, 13, 1, 6, 30, 30, 30, 30, 30, 30, 37, 37, 37, 30, 30, 6, 1, 1, 1, 1, 13, 28, 28, 37, 37, 1, 1, 30, 30, 30, 30, 37, 37, 37, 37, 37, 37, 37, 30, 30, 30, 30] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 41, 42, 34, 18, 35] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113869 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@H]1CC[C@H](C2CCC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 30, 30, 30, 141, 141, 141, 175, 201, 201, 201, 201, 201, 141, 141, 30, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 10, 30, 30, 30, 30, 141, 175, 175, 201, 201, 30, 30, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1] 201 rigid atoms, others: [1, 54, 57, 43, 44, 45, 46, 56, 19, 20, 21, 22, 23, 24, 25, 55, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 564 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113869 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113869/1 /scratch/stefan/7770410/working/building/REAL300020113869 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1353) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1353 `/scratch/stefan/7770410/working/3D/1353' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@H]1CC[C@H](C2CCC2)CC1) `REAL300020113869.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113869/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113869 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@H]1CC[C@H](C2CCC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 13, 48, 141, 141, 141, 141, 141, 141, 144, 144, 144, 141, 141, 48, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 141, 141, 141, 141, 144, 144, 144, 144, 144, 144, 144, 141, 141, 141, 141] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 432 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113869 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@H]1CC[C@H](C2CCC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 2, 16, 16, 37, 37, 37, 144, 144, 144, 174, 201, 201, 201, 201, 201, 144, 144, 37, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 2, 2, 16, 37, 37, 37, 37, 144, 174, 174, 201, 201, 37, 37, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2] 201 rigid atoms, others: [47, 48, 49, 50, 51, 52, 53, 23, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 54, 55, 56, 57]) total number of confs: 559 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113869 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@H]1CC[C@H](C2CCC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 39, 39, 39, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 39, 97, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 97, 39, 39, 39, 39, 8, 4, 4, 2, 2, 39, 39, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 607 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113869 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@H]1CC[C@H](C2CCC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 28, 37, 37, 37, 37, 37, 13, 13, 1, 6, 30, 30, 30, 30, 30, 30, 37, 37, 37, 30, 30, 6, 1, 1, 1, 1, 13, 28, 28, 37, 37, 1, 1, 30, 30, 30, 30, 37, 37, 37, 37, 37, 37, 37, 30, 30, 30, 30] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 41, 42, 34, 18, 35] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113869 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@H]1CC[C@H](C2CCC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 30, 30, 30, 141, 141, 141, 174, 201, 201, 201, 201, 201, 141, 141, 30, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 10, 30, 30, 30, 30, 141, 174, 174, 201, 201, 30, 30, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1] 201 rigid atoms, others: [1, 54, 57, 43, 44, 45, 46, 56, 19, 20, 21, 22, 23, 24, 25, 55, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 561 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113869 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113869 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113869/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113869/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113869 Building REAL300020113870 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113870' /scratch/stefan/7770410/working/building/REAL300020113870 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113870 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113870/0 /scratch/stefan/7770410/working/building/REAL300020113870 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1354) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1354 `/scratch/stefan/7770410/working/3D/1354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=NC2=CN=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=C21) `REAL300020113870.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113870 none CN1C=NC2=CN=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 35, 53, 61, 61, 61, 61, 13, 13, 1, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 13, 35, 35, 53, 53, 1, 1] 201 rigid atoms, others: [45, 36, 37, 38, 39, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 267 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113870 none CN1C=NC2=CN=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 107, 107, 107, 107, 47, 47, 47, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 13, 107, 107, 107, 107, 107, 107, 107, 47, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13] 201 rigid atoms, others: [40, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 240 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113870 none CN1C=NC2=CN=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 22, 22, 22, 107, 107, 107, 166, 201, 201, 201, 201, 201, 107, 107, 22, 1, 2, 2, 2, 1, 1, 1, 7, 22, 22, 22, 22, 107, 166, 166, 201, 201, 22, 22] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 34, 33, 28] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 693 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113870 none CN1C=NC2=CN=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 139, 139, 139, 62, 62, 62, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 62, 201, 201, 201, 201, 201, 201, 201, 139, 62, 62, 62, 62, 10, 6, 6, 4, 4, 62, 62] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 501 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113870 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113870/1 /scratch/stefan/7770410/working/building/REAL300020113870 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1355) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1355 `/scratch/stefan/7770410/working/3D/1355' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=NC2=CN=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=C21) `REAL300020113870.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113870/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113870 none CN1C=NC2=CN=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 36, 54, 61, 61, 61, 61, 13, 13, 1, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 13, 36, 36, 54, 54, 1, 1] 201 rigid atoms, others: [45, 36, 37, 38, 39, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 268 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113870 none CN1C=NC2=CN=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 106, 106, 106, 106, 106, 47, 47, 47, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 106, 106, 106, 106, 106, 106, 106, 47, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [40, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 242 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113870 none CN1C=NC2=CN=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 22, 22, 22, 106, 106, 106, 167, 201, 201, 201, 201, 201, 106, 106, 22, 1, 2, 2, 2, 1, 1, 1, 7, 22, 22, 22, 22, 106, 167, 167, 201, 201, 22, 22] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 34, 33, 28] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 696 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113870 none CN1C=NC2=CN=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 139, 139, 139, 62, 62, 62, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 62, 201, 201, 201, 201, 201, 201, 201, 139, 62, 62, 62, 62, 10, 6, 6, 4, 4, 62, 62] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 501 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113870 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113870 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113870/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113870/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113870 Building REAL300020113871 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113871' /scratch/stefan/7770410/working/building/REAL300020113871 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for REAL300020113871 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113871/0 /scratch/stefan/7770410/working/building/REAL300020113871 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1356) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1356 `/scratch/stefan/7770410/working/3D/1356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@@H+]1CCCC1CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113871.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113871 none C[N@@H+]1CCCC1CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 6, 8, 3, 3, 3, 1, 1, 1, 1, 1, 8, 8, 8, 9, 9, 9, 9, 9, 9, 8, 8, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8, 8, 8, 8, 3, 1, 1, 1, 1, 8, 9, 9, 9, 9, 1, 1] 17 rigid atoms, others: [11, 15, 44, 43, 12, 13, 14, 45, 52, 46, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 60 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113871 none C[N@@H+]1CCCC1CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 14, 17, 10, 10, 10, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 8, 8, 8, 8, 1, 3, 3, 3, 3, 8, 8] 17 rigid atoms, others: [14, 47, 16, 17, 18, 25, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 82 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113871 none C[N@@H+]1CCCC1CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 11, 11] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 35, 36, 33, 37, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113871 none C[N@@H+]1CCCC1CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 8, 10, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6, 6, 3, 3, 3, 1, 1, 6, 6] 10 rigid atoms, others: [19, 50, 18, 51, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 51 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113871 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113871/1 /scratch/stefan/7770410/working/building/REAL300020113871 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1357) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1357 `/scratch/stefan/7770410/working/3D/1357' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@H+]1CCCC1CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113871.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113871 none C[N@H+]1CCCC1CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1] 2 rigid atoms, others: [11, 15, 44, 43, 12, 13, 14, 45, 52, 46, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 7 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113871 none C[N@H+]1CCCC1CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2] 2 rigid atoms, others: [14, 47, 16, 17, 18, 25, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 11 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113871 none C[N@H+]1CCCC1CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 2 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 35, 36, 33, 37, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 13 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113871 none C[N@H+]1CCCC1CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 2, 2] 2 rigid atoms, others: [19, 50, 18, 51, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 7 number of broken/clashed sets: 2 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113871 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `2' /scratch/stefan/7770410/working/building/REAL300020113871/2 /scratch/stefan/7770410/working/building/REAL300020113871 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 2 (index: 1358) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1358 `/scratch/stefan/7770410/working/3D/1358' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@@H+]1CCCC1CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113871.mol2' -> `2.mol2' `temp.mol2' -> `REAL300020113871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113871/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113871 none C[N@@H+]1CCCC1CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 6, 8, 3, 3, 3, 1, 1, 1, 1, 1, 8, 8, 8, 9, 9, 9, 9, 9, 9, 8, 8, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8, 8, 8, 8, 3, 1, 1, 1, 1, 8, 9, 9, 9, 9, 1, 1] 17 rigid atoms, others: [11, 15, 44, 43, 12, 13, 14, 45, 52, 46, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 60 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113871 none C[N@@H+]1CCCC1CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 14, 17, 10, 10, 10, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 8, 8, 8, 8, 1, 3, 3, 3, 3, 8, 8] 17 rigid atoms, others: [14, 47, 16, 17, 18, 25, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 82 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113871 none C[N@@H+]1CCCC1CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 11, 11] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 35, 36, 33, 37, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113871 none C[N@@H+]1CCCC1CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 8, 10, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6, 6, 3, 3, 3, 1, 1, 6, 6] 10 rigid atoms, others: [19, 50, 18, 51, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 51 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113871 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `3' /scratch/stefan/7770410/working/building/REAL300020113871/3 /scratch/stefan/7770410/working/building/REAL300020113871 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 3 (index: 1359) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1359 `/scratch/stefan/7770410/working/3D/1359' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@H+]1CCCC1CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113871.mol2' -> `3.mol2' `temp.mol2' -> `REAL300020113871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113871/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113871 none C[N@H+]1CCCC1CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1] 2 rigid atoms, others: [11, 15, 44, 43, 12, 13, 14, 45, 52, 46, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 7 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113871 none C[N@H+]1CCCC1CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2] 2 rigid atoms, others: [14, 47, 16, 17, 18, 25, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 11 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113871 none C[N@H+]1CCCC1CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 2 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 35, 36, 33, 37, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 13 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113871 none C[N@H+]1CCCC1CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 2, 2] 2 rigid atoms, others: [19, 50, 18, 51, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 7 number of broken/clashed sets: 2 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113871 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113871 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 2: /scratch/stefan/7770410/working/building/REAL300020113871/2.* 1: /scratch/stefan/7770410/working/building/REAL300020113871/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113871/0.* 3: /scratch/stefan/7770410/working/building/REAL300020113871/3.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113871 Building REAL300020113872 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113872' /scratch/stefan/7770410/working/building/REAL300020113872 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113872 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113872/0 /scratch/stefan/7770410/working/building/REAL300020113872 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1360) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1360 `/scratch/stefan/7770410/working/3D/1360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCNC1=O) `REAL300020113872.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113872 none CCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 9, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 63, 86, 108, 108, 108, 108, 13, 13, 1, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 13, 63, 63, 86, 86, 1, 1, 9, 9, 9, 9, 9] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 42, 43, 21] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48]) total number of confs: 430 number of broken/clashed sets: 34 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113872 none CCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 58, 53, 53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 19, 19, 19, 19, 1, 1, 13, 58, 58, 58, 58, 58, 76, 76, 76, 76, 76, 53, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 58, 58, 58, 58, 58] 201 rigid atoms, others: [37, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 322 number of broken/clashed sets: 34 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113872 none CCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 4, 4, 4, 9, 9, 9, 58, 58, 58, 158, 194, 201, 201, 201, 201, 58, 58, 9, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 58, 158, 158, 194, 194, 9, 9, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 44, 45, 46, 47, 48, 22, 23, 24, 25, 26] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 747 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113872 none CCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [155, 155, 155, 155, 155, 91, 91, 91, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 91, 155, 155, 155, 155, 155, 155, 155, 155, 155, 155, 155, 91, 91, 91, 91, 15, 6, 6, 4, 4, 91, 91, 155, 155, 155, 155, 155] 155 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 429 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113872 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113872/1 /scratch/stefan/7770410/working/building/REAL300020113872 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1361) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1361 `/scratch/stefan/7770410/working/3D/1361' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCNC1=O) `REAL300020113872.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113872/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113872 none CCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 9, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 63, 86, 108, 108, 108, 108, 13, 13, 1, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 13, 63, 63, 86, 86, 1, 1, 9, 9, 9, 9, 9] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 42, 43, 21] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48]) total number of confs: 430 number of broken/clashed sets: 34 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113872 none CCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 58, 53, 53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 19, 19, 19, 19, 1, 1, 13, 58, 58, 58, 58, 58, 76, 76, 76, 76, 76, 53, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 58, 58, 58, 58, 58] 201 rigid atoms, others: [37, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 322 number of broken/clashed sets: 34 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113872 none CCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 4, 4, 4, 9, 9, 9, 58, 58, 58, 158, 194, 201, 201, 201, 201, 58, 58, 9, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 58, 158, 158, 194, 194, 9, 9, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 44, 45, 46, 47, 48, 22, 23, 24, 25, 26] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 747 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113872 none CCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [155, 155, 155, 155, 155, 90, 90, 90, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 90, 155, 155, 155, 155, 155, 155, 155, 155, 155, 155, 155, 90, 90, 90, 90, 14, 6, 6, 4, 4, 90, 90, 155, 155, 155, 155, 155] 155 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 432 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113872 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113872 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113872/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113872/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113872 Building REAL300020113873 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113873' /scratch/stefan/7770410/working/building/REAL300020113873 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113873 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113873/0 /scratch/stefan/7770410/working/building/REAL300020113873 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1362) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1362 `/scratch/stefan/7770410/working/3D/1362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113873.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113873 none CC[C@@H]1CCO[C@@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 6, 12, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 39, 57, 64, 64, 64, 64, 13, 13, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 13, 39, 39, 57, 57, 1, 1] 180 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 284 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113873 none CC[C@@H]1CCO[C@@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 96, 96, 96, 96, 59, 96, 59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 13, 96, 96, 96, 96, 96, 96, 96, 96, 96, 59, 13, 13, 13, 13, 1, 7, 7, 9, 9, 13, 13] 180 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 328 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113873 none CC[C@@H]1CCO[C@@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 96, 96, 96, 153, 180, 180, 180, 180, 180, 96, 96, 12, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 12, 12, 12, 12, 96, 153, 153, 180, 180, 12, 12] 180 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 36, 33] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 586 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113873 none CC[C@@H]1CCO[C@@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [180, 180, 180, 180, 180, 180, 180, 163, 180, 163, 163, 64, 64, 64, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 64, 180, 180, 180, 180, 180, 180, 180, 180, 180, 163, 64, 64, 64, 64, 12, 6, 6, 4, 4, 64, 64] 180 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 514 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113873 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113873/1 /scratch/stefan/7770410/working/building/REAL300020113873 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1363) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1363 `/scratch/stefan/7770410/working/3D/1363' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113873.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113873/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113873 none CC[C@@H]1CCO[C@@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 6, 12, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 39, 57, 64, 64, 64, 64, 13, 13, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 13, 39, 39, 57, 57, 1, 1] 179 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 284 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113873 none CC[C@@H]1CCO[C@@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 96, 96, 96, 96, 59, 96, 59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 13, 96, 96, 96, 96, 96, 96, 96, 96, 96, 59, 13, 13, 13, 13, 1, 7, 7, 9, 9, 13, 13] 179 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 328 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113873 none CC[C@@H]1CCO[C@@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 96, 96, 96, 153, 179, 179, 179, 179, 179, 96, 96, 12, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 12, 12, 12, 12, 96, 153, 153, 179, 179, 12, 12] 179 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 36, 33] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 580 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113873 none CC[C@@H]1CCO[C@@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [178, 178, 178, 178, 178, 178, 178, 161, 178, 161, 161, 63, 63, 63, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 63, 178, 178, 178, 178, 178, 178, 178, 178, 178, 161, 63, 63, 63, 63, 12, 6, 6, 4, 4, 63, 63] 178 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 510 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113873 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113873 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113873/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113873/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113873 Building REAL300020113874 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113874' /scratch/stefan/7770410/working/building/REAL300020113874 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113874 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113874/0 /scratch/stefan/7770410/working/building/REAL300020113874 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1364) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1364 `/scratch/stefan/7770410/working/3D/1364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC=CCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113874.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113874 none O=C(CC=CCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 19, 23, 23, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 1, 7, 7, 7, 20, 32, 32, 32, 32, 32, 7, 7, 1, 19, 19, 23, 23, 54, 54, 54, 54, 54, 54, 54, 5, 1, 1, 1, 1, 7, 20, 20, 32, 32, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 350 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113874 none O=C(CC=CCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 61, 65, 65, 124, 124, 124, 124, 124, 124, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 61, 61, 65, 65, 124, 124, 124, 124, 124, 124, 124, 17, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 558 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113874 none O=C(CC=CCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 54, 54, 54, 124, 124, 124, 173, 201, 201, 201, 201, 201, 124, 124, 54, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 33, 54, 54, 54, 54, 124, 173, 173, 201, 201, 54, 54] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 36, 38, 39, 37] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 705 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113874 none O=C(CC=CCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 135, 141, 141, 201, 201, 201, 201, 201, 201, 33, 33, 33, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 33, 135, 135, 141, 141, 201, 201, 201, 201, 201, 201, 201, 50, 33, 33, 33, 33, 9, 4, 4, 2, 2, 33, 33] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 823 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113874 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113874/1 /scratch/stefan/7770410/working/building/REAL300020113874 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1365) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1365 `/scratch/stefan/7770410/working/3D/1365' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC=CCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113874.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113874/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113874 none O=C(CC=CCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 19, 23, 23, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 1, 7, 7, 7, 19, 31, 31, 31, 31, 31, 7, 7, 1, 19, 19, 23, 23, 54, 54, 54, 54, 54, 54, 54, 5, 1, 1, 1, 1, 7, 19, 19, 31, 31, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 347 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113874 none O=C(CC=CCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 61, 65, 65, 124, 124, 124, 124, 124, 124, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 61, 61, 65, 65, 124, 124, 124, 124, 124, 124, 124, 17, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 555 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113874 none O=C(CC=CCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 54, 54, 54, 124, 124, 124, 173, 201, 201, 201, 201, 201, 124, 124, 54, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 33, 54, 54, 54, 54, 124, 173, 173, 201, 201, 54, 54] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 36, 38, 39, 37] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 705 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113874 none O=C(CC=CCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 134, 140, 140, 201, 201, 201, 201, 201, 201, 34, 34, 34, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 34, 134, 134, 140, 140, 201, 201, 201, 201, 201, 201, 201, 51, 34, 34, 34, 34, 9, 4, 4, 2, 2, 34, 34] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 821 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113874 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113874 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113874/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113874/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113874 Building REAL300020113875 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113875' /scratch/stefan/7770410/working/building/REAL300020113875 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113875 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113875/0 /scratch/stefan/7770410/working/building/REAL300020113875 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1366) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1366 `/scratch/stefan/7770410/working/3D/1366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1=CNC=N1) `REAL300020113875.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113875 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1=CNC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 10, 35, 105, 105, 105, 105, 105, 153, 153, 153, 153, 35, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 105, 105, 153, 153, 153] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 400 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113875 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1=CNC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 8, 29, 29, 62, 62, 62, 153, 153, 153, 194, 201, 201, 201, 201, 201, 153, 153, 62, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 29, 62, 62, 62, 62, 153, 194, 194, 201, 201, 62, 62, 8, 8, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 22, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 579 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113875 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1=CNC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 39, 39, 39, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 39, 99, 200, 200, 200, 200, 200, 201, 201, 201, 201, 99, 39, 39, 39, 39, 9, 4, 4, 2, 2, 39, 39, 200, 200, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 587 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113875 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1=CNC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 26, 37, 37, 37, 37, 37, 10, 10, 1, 6, 25, 25, 25, 25, 25, 62, 62, 62, 62, 6, 1, 1, 1, 1, 10, 26, 26, 37, 37, 1, 1, 25, 25, 62, 62, 62] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 259 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113875 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1=CNC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 25, 25, 25, 105, 105, 105, 165, 193, 193, 193, 193, 193, 105, 105, 25, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 25, 25, 25, 25, 105, 165, 165, 193, 193, 25, 25, 1, 1, 8, 8, 8] 201 rigid atoms, others: [1, 41, 42, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 662 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113875 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113875/1 /scratch/stefan/7770410/working/building/REAL300020113875 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1367) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1367 `/scratch/stefan/7770410/working/3D/1367' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1=CNC=N1) `REAL300020113875.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113875/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113875 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1=CNC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 10, 35, 105, 105, 105, 105, 105, 154, 154, 154, 154, 35, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 105, 105, 154, 154, 154] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 402 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113875 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1=CNC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 8, 29, 29, 62, 62, 62, 154, 154, 154, 193, 201, 201, 201, 201, 201, 154, 154, 62, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 29, 62, 62, 62, 62, 154, 193, 193, 201, 201, 62, 62, 8, 8, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 22, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 577 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113875 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1=CNC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 38, 38, 38, 10, 10, 10, 4, 2, 1, 1, 1, 1, 1, 1, 10, 10, 38, 98, 200, 200, 200, 200, 200, 201, 201, 201, 201, 98, 38, 38, 38, 38, 10, 4, 4, 2, 2, 38, 38, 200, 200, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 586 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113875 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1=CNC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 26, 37, 37, 37, 37, 37, 10, 10, 1, 6, 25, 25, 25, 25, 25, 62, 62, 62, 62, 6, 1, 1, 1, 1, 10, 26, 26, 37, 37, 1, 1, 25, 25, 62, 62, 62] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 259 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113875 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1=CNC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 25, 25, 25, 105, 105, 105, 163, 193, 193, 193, 193, 193, 105, 105, 25, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 25, 25, 25, 25, 105, 163, 163, 193, 193, 25, 25, 1, 1, 8, 8, 8] 201 rigid atoms, others: [1, 41, 42, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 665 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113875 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113875 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113875/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113875/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113875 Building REAL300020113876 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113876' /scratch/stefan/7770410/working/building/REAL300020113876 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113876 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113876/0 /scratch/stefan/7770410/working/building/REAL300020113876 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1368) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1368 `/scratch/stefan/7770410/working/3D/1368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2SC=CC2=CC=N1) `REAL300020113876.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113876 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2SC=CC2=CC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 13, 60, 121, 121, 121, 121, 121, 121, 121, 121, 60, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 121, 121, 121, 121] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 275 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113876 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2SC=CC2=CC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [179, 179, 57, 57, 57, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 57, 179, 201, 201, 201, 201, 201, 201, 201, 201, 179, 57, 57, 57, 57, 10, 5, 5, 3, 3, 57, 57, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 517 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113876 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2SC=CC2=CC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 39, 54, 55, 55, 55, 55, 13, 13, 1, 6, 25, 25, 25, 25, 25, 25, 25, 25, 6, 1, 1, 1, 1, 13, 39, 39, 54, 54, 1, 1, 25, 25, 25, 25] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113876 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2SC=CC2=CC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 25, 25, 25, 121, 121, 121, 176, 201, 201, 201, 201, 201, 121, 121, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 25, 25, 25, 25, 121, 176, 176, 201, 201, 25, 25, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 618 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113876 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113876/1 /scratch/stefan/7770410/working/building/REAL300020113876 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1369) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1369 `/scratch/stefan/7770410/working/3D/1369' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2SC=CC2=CC=N1) `REAL300020113876.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113876 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2SC=CC2=CC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 13, 60, 121, 121, 121, 121, 121, 121, 121, 121, 60, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 121, 121, 121, 121] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 275 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113876 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2SC=CC2=CC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [178, 178, 57, 57, 57, 11, 11, 11, 5, 3, 1, 1, 1, 1, 1, 1, 11, 11, 57, 178, 201, 201, 201, 201, 201, 201, 201, 201, 178, 57, 57, 57, 57, 11, 5, 5, 3, 3, 57, 57, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 516 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113876 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2SC=CC2=CC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 40, 55, 56, 56, 56, 56, 13, 13, 1, 6, 25, 25, 25, 25, 25, 25, 25, 25, 6, 1, 1, 1, 1, 13, 40, 40, 55, 55, 1, 1, 25, 25, 25, 25] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 259 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113876 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2SC=CC2=CC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 25, 25, 25, 121, 121, 121, 177, 201, 201, 201, 201, 201, 121, 121, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 25, 25, 25, 25, 121, 177, 177, 201, 201, 25, 25, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 615 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113876 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113876 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113876/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113876/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113876 Building REAL300020113877 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113877' /scratch/stefan/7770410/working/building/REAL300020113877 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113877 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113877/0 /scratch/stefan/7770410/working/building/REAL300020113877 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1370) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1370 `/scratch/stefan/7770410/working/3D/1370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2COCCN12) `REAL300020113877.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113877 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2COCCN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 12, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 17, 17, 17, 17, 1, 1, 12, 48, 105, 105, 105, 105, 105, 105, 105, 105, 48, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 105, 105, 105, 105, 105, 105, 105] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 257 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113877 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2COCCN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 12, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [175, 175, 96, 96, 96, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 96, 175, 201, 201, 201, 201, 201, 201, 201, 201, 175, 96, 96, 96, 96, 17, 6, 6, 4, 4, 96, 96, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 522 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113877 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2COCCN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 12, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 55, 74, 95, 95, 95, 95, 12, 12, 1, 6, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 12, 55, 55, 74, 74, 1, 1, 20, 20, 20, 20, 20, 20, 20] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113877 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2COCCN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 12, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 20, 20, 20, 105, 105, 105, 172, 201, 201, 201, 201, 201, 105, 105, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 20, 20, 20, 20, 105, 172, 172, 201, 201, 20, 20, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 674 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113877 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113877/1 /scratch/stefan/7770410/working/building/REAL300020113877 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1371) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1371 `/scratch/stefan/7770410/working/3D/1371' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2COCCN12) `REAL300020113877.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113877 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2COCCN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 12, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 17, 17, 17, 17, 1, 1, 12, 48, 106, 106, 106, 106, 106, 106, 106, 106, 48, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 106, 106, 106, 106, 106, 106, 106] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 259 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113877 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2COCCN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 12, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [175, 175, 96, 96, 96, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 96, 175, 201, 201, 201, 201, 201, 201, 201, 201, 175, 96, 96, 96, 96, 17, 6, 6, 4, 4, 96, 96, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 522 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113877 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2COCCN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 12, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 56, 75, 96, 96, 96, 96, 12, 12, 1, 6, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 12, 56, 56, 75, 75, 1, 1, 20, 20, 20, 20, 20, 20, 20] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 365 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113877 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2COCCN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 12, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 20, 20, 20, 106, 106, 106, 172, 201, 201, 201, 201, 201, 106, 106, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 20, 20, 20, 20, 106, 172, 172, 201, 201, 20, 20, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 672 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113877 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113877 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113877/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113877/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113877 Building REAL300020113878 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113878' /scratch/stefan/7770410/working/building/REAL300020113878 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113878 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113878/0 /scratch/stefan/7770410/working/building/REAL300020113878 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1372) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1372 `/scratch/stefan/7770410/working/3D/1372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=C2CCCCN2N=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113878.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113878 none O=C(CC1=C2CCCCN2N=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 5, 5, 5, 5, 8, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 23, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 8, 8, 8, 20, 31, 31, 31, 31, 31, 8, 8, 1, 23, 23, 41, 41, 41, 41, 41, 41, 41, 41, 41, 5, 1, 1, 1, 1, 8, 20, 20, 31, 31, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 237 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113878 none O=C(CC1=C2CCCCN2N=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 5, 5, 5, 5, 8, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 77, 126, 126, 126, 126, 126, 126, 126, 126, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 77, 77, 126, 126, 126, 126, 126, 126, 126, 126, 126, 18, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 379 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113878 none O=C(CC1=C2CCCCN2N=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 5, 5, 5, 5, 8, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 41, 41, 41, 126, 126, 126, 177, 201, 201, 201, 201, 201, 126, 126, 41, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 41, 41, 41, 41, 126, 177, 177, 201, 201, 41, 41] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 36, 38, 37, 39, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 676 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113878 none O=C(CC1=C2CCCCN2N=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 5, 5, 5, 5, 8, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 141, 201, 201, 201, 201, 201, 201, 201, 201, 32, 32, 32, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 32, 141, 141, 201, 201, 201, 201, 201, 201, 201, 201, 201, 47, 32, 32, 32, 32, 8, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 629 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113878 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113878/1 /scratch/stefan/7770410/working/building/REAL300020113878 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1373) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1373 `/scratch/stefan/7770410/working/3D/1373' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=C2CCCCN2N=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113878.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113878 none O=C(CC1=C2CCCCN2N=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 5, 5, 5, 5, 8, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 23, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 1, 8, 8, 8, 20, 31, 31, 31, 31, 31, 8, 8, 1, 23, 23, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 1, 1, 1, 1, 8, 20, 20, 31, 31, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 238 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113878 none O=C(CC1=C2CCCCN2N=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 5, 5, 5, 5, 8, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 77, 128, 128, 128, 128, 128, 128, 128, 128, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 77, 77, 128, 128, 128, 128, 128, 128, 128, 128, 128, 18, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 382 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113878 none O=C(CC1=C2CCCCN2N=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 5, 5, 5, 5, 8, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 42, 42, 42, 128, 128, 128, 178, 201, 201, 201, 201, 201, 128, 128, 42, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 42, 42, 42, 42, 128, 178, 178, 201, 201, 42, 42] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 36, 38, 37, 39, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 669 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113878 none O=C(CC1=C2CCCCN2N=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 5, 5, 5, 5, 8, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 140, 201, 201, 201, 201, 201, 201, 201, 201, 32, 32, 32, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 32, 140, 140, 201, 201, 201, 201, 201, 201, 201, 201, 201, 47, 32, 32, 32, 32, 8, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 627 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113878 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113878 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113878/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113878/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113878 Building REAL300020113879 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113879' /scratch/stefan/7770410/working/building/REAL300020113879 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113879 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113879/0 /scratch/stefan/7770410/working/building/REAL300020113879 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1374) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1374 `/scratch/stefan/7770410/working/3D/1374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)OC(C(F)F)=C1) `REAL300020113879.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113879 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)OC(C(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 8, 8, 8, 6, 6, 1, 29, 29, 29, 39, 39, 29, 29, 29, 29, 6, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 39, 29] 43 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 42, 21, 41] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44]) total number of confs: 116 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113879 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)OC(C(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 6, 39, 39, 39, 41, 41, 39, 39, 39, 39, 16, 6, 6, 6, 6, 1, 5, 5, 5, 5, 6, 6, 41, 39] 43 rigid atoms, others: [36, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 102 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113879 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)OC(C(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 29, 29, 29, 39, 39, 39, 43, 43, 43, 43, 43, 43, 39, 39, 29, 1, 1, 1, 11, 11, 1, 2, 2, 2, 9, 29, 29, 29, 29, 39, 43, 43, 43, 43, 29, 29, 11, 1] 43 rigid atoms, others: [0, 1, 2, 3, 44, 22, 23, 24, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113879 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)OC(C(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 19, 19, 19, 9, 9, 9, 6, 6, 6, 4, 2, 1, 1, 1, 1, 1, 1, 6, 6, 9, 43, 43, 43, 43, 43, 43, 43, 43, 43, 19, 9, 9, 9, 9, 6, 4, 4, 2, 2, 9, 9, 43, 43] 43 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 97 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113879 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113879/1 /scratch/stefan/7770410/working/building/REAL300020113879 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1375) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1375 `/scratch/stefan/7770410/working/3D/1375' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)OC(C(F)F)=C1) `REAL300020113879.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113879 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)OC(C(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 8, 8, 8, 6, 6, 1, 29, 29, 29, 39, 39, 29, 29, 29, 29, 6, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 39, 29] 43 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 42, 21, 41] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44]) total number of confs: 116 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113879 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)OC(C(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 6, 39, 39, 39, 41, 41, 39, 39, 39, 39, 16, 6, 6, 6, 6, 1, 5, 5, 5, 5, 6, 6, 41, 39] 43 rigid atoms, others: [36, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 102 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113879 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)OC(C(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 29, 29, 29, 39, 39, 39, 43, 43, 43, 43, 43, 43, 39, 39, 29, 1, 1, 1, 11, 11, 1, 2, 2, 2, 9, 29, 29, 29, 29, 39, 43, 43, 43, 43, 29, 29, 11, 1] 43 rigid atoms, others: [0, 1, 2, 3, 44, 22, 23, 24, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113879 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)OC(C(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.3', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 1, 5, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 19, 19, 19, 9, 9, 9, 6, 6, 6, 4, 2, 1, 1, 1, 1, 1, 1, 6, 6, 9, 43, 43, 43, 43, 43, 43, 43, 43, 43, 19, 9, 9, 9, 9, 6, 4, 4, 2, 2, 9, 9, 43, 43] 43 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 97 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113879 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113879 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113879/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113879/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113879 Building REAL300020113880 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113880' /scratch/stefan/7770410/working/building/REAL300020113880 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113880 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113880/0 /scratch/stefan/7770410/working/building/REAL300020113880 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1376) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1376 `/scratch/stefan/7770410/working/3D/1376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC=CCCC1) `REAL300020113880.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113880 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC=CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 52, 145, 145, 145, 145, 145, 145, 145, 52, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 145, 145, 145, 145, 145, 145, 145, 145, 145, 145, 145, 145, 145] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 435 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113880 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC=CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [121, 121, 44, 44, 44, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 44, 121, 201, 201, 201, 201, 201, 201, 201, 121, 44, 44, 44, 44, 8, 4, 4, 2, 2, 44, 44, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 611 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113880 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC=CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 34, 44, 44, 44, 44, 44, 13, 13, 1, 6, 29, 29, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 13, 34, 34, 44, 44, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 235 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113880 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC=CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 29, 29, 29, 145, 145, 145, 191, 201, 201, 201, 201, 201, 145, 145, 29, 1, 1, 1, 1, 1, 1, 1, 1, 10, 29, 29, 29, 29, 145, 191, 191, 201, 201, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 538 number of broken/clashed sets: 201 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113880 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113880/1 /scratch/stefan/7770410/working/building/REAL300020113880 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1377) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1377 `/scratch/stefan/7770410/working/3D/1377' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC=CCCC1) `REAL300020113880.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113880 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC=CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 52, 145, 145, 145, 145, 145, 145, 145, 52, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 145, 145, 145, 145, 145, 145, 145, 145, 145, 145, 145, 145, 145] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 435 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113880 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC=CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [121, 121, 44, 44, 44, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 44, 121, 201, 201, 201, 201, 201, 201, 201, 121, 44, 44, 44, 44, 8, 4, 4, 2, 2, 44, 44, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 611 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113880 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC=CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 34, 44, 44, 44, 44, 44, 13, 13, 1, 6, 29, 29, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 13, 34, 34, 44, 44, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 235 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113880 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC=CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 29, 29, 29, 145, 145, 145, 191, 201, 201, 201, 201, 201, 145, 145, 29, 1, 1, 1, 1, 1, 1, 1, 1, 10, 29, 29, 29, 29, 145, 191, 191, 201, 201, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 538 number of broken/clashed sets: 201 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113880 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113880 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113880/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113880/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113880 Building REAL300020113881 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113881' /scratch/stefan/7770410/working/building/REAL300020113881 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113881 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113881/0 /scratch/stefan/7770410/working/building/REAL300020113881 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1378) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1378 `/scratch/stefan/7770410/working/3D/1378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN(C(C)(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1) `REAL300020113881.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113881 none CC1=CN(C(C)(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 25, 37, 40, 40, 40, 40, 9, 9, 1, 33, 33, 33, 33, 33, 33, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 9, 25, 25, 37, 37, 1, 1, 33] 201 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 48, 49, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50]) total number of confs: 226 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113881 none CC1=CN(C(C)(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 54, 25, 54, 54, 25, 25, 9, 9, 9, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 9, 113, 113, 113, 113, 113, 113, 54, 54, 54, 54, 54, 54, 25, 9, 9, 9, 9, 1, 5, 5, 7, 7, 9, 9, 113] 201 rigid atoms, others: [43, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 318 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113881 none CC1=CN(C(C)(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 10, 15, 15, 15, 33, 33, 33, 113, 113, 113, 169, 201, 201, 201, 201, 201, 113, 113, 33, 1, 1, 2, 2, 2, 1, 10, 10, 10, 10, 10, 10, 15, 33, 33, 33, 33, 113, 169, 169, 201, 201, 33, 33, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 50, 26, 27, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 716 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113881 none CC1=CN(C(C)(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 138, 76, 138, 138, 76, 76, 42, 42, 42, 11, 11, 11, 7, 4, 1, 1, 1, 1, 1, 1, 11, 11, 42, 201, 201, 201, 201, 201, 201, 138, 138, 138, 138, 138, 138, 76, 42, 42, 42, 42, 11, 7, 7, 4, 4, 42, 42, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 654 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113881 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113881/1 /scratch/stefan/7770410/working/building/REAL300020113881 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1379) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1379 `/scratch/stefan/7770410/working/3D/1379' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN(C(C)(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1) `REAL300020113881.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113881 none CC1=CN(C(C)(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 15, 6, 15, 15, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 26, 38, 41, 41, 41, 41, 9, 9, 1, 34, 34, 34, 34, 34, 34, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 9, 26, 26, 38, 38, 1, 1, 34] 201 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 48, 49, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50]) total number of confs: 238 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113881 none CC1=CN(C(C)(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 115, 55, 25, 55, 55, 25, 25, 9, 9, 9, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 9, 115, 115, 115, 115, 115, 115, 55, 55, 55, 55, 55, 55, 25, 9, 9, 9, 9, 1, 5, 5, 7, 7, 9, 9, 115] 201 rigid atoms, others: [43, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 325 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113881 none CC1=CN(C(C)(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 10, 15, 15, 15, 34, 34, 34, 115, 115, 115, 171, 201, 201, 201, 201, 201, 115, 115, 34, 1, 1, 2, 2, 2, 1, 10, 10, 10, 10, 10, 10, 15, 34, 34, 34, 34, 115, 171, 171, 201, 201, 34, 34, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 50, 26, 27, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 707 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113881 none CC1=CN(C(C)(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 137, 77, 137, 137, 77, 77, 43, 43, 43, 11, 11, 11, 7, 4, 1, 1, 1, 1, 1, 1, 11, 11, 43, 201, 201, 201, 201, 201, 201, 137, 137, 137, 137, 137, 137, 77, 43, 43, 43, 43, 11, 7, 7, 4, 4, 43, 43, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 646 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113881 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113881 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113881/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113881/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113881 Building REAL300020113882 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113882' /scratch/stefan/7770410/working/building/REAL300020113882 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113882 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113882/0 /scratch/stefan/7770410/working/building/REAL300020113882 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1380) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1380 `/scratch/stefan/7770410/working/3D/1380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C12CCC[NH+](CCC1)C2) `REAL300020113882.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113882 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C12CCC[NH+](CCC1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 9, 9, 9, 1, 1, 1, 1, 1, 4, 6, 6, 6, 6, 6, 1, 1, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 1, 4, 4, 6, 6, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 44 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 85 number of broken/clashed sets: 44 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113882 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C12CCC[NH+](CCC1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 18, 18, 18, 6, 6, 6, 4, 2, 1, 1, 1, 1, 1, 1, 6, 6, 18, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 18, 18, 18, 18, 6, 4, 4, 2, 2, 18, 18, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44] 44 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 126 number of broken/clashed sets: 44 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113882 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C12CCC[NH+](CCC1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 1, 9, 9, 9, 16, 18, 18, 18, 18, 18, 9, 9, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 9, 16, 16, 18, 18, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 44 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 69 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113882 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C12CCC[NH+](CCC1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 23, 23, 23, 42, 44, 44, 44, 44, 44, 23, 23, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 23, 42, 42, 44, 44, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 44 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 156 number of broken/clashed sets: 44 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113882 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113882/1 /scratch/stefan/7770410/working/building/REAL300020113882 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1381) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1381 `/scratch/stefan/7770410/working/3D/1381' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C12CCC[NH+](CCC1)C2) `REAL300020113882.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113882 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C12CCC[NH+](CCC1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 9, 9, 9, 1, 1, 1, 1, 1, 4, 6, 6, 6, 6, 6, 1, 1, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 1, 4, 4, 6, 6, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 44 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 85 number of broken/clashed sets: 44 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113882 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C12CCC[NH+](CCC1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 18, 18, 18, 6, 6, 6, 4, 2, 1, 1, 1, 1, 1, 1, 6, 6, 18, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 18, 18, 18, 18, 6, 4, 4, 2, 2, 18, 18, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44] 44 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 126 number of broken/clashed sets: 44 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113882 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C12CCC[NH+](CCC1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 1, 9, 9, 9, 16, 18, 18, 18, 18, 18, 9, 9, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 9, 16, 16, 18, 18, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 44 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 69 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113882 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C12CCC[NH+](CCC1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 23, 23, 23, 42, 44, 44, 44, 44, 44, 23, 23, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 23, 42, 42, 44, 44, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 44 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 156 number of broken/clashed sets: 44 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113882 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113882 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113882/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113882/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113882 Building REAL300020113883 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113883' /scratch/stefan/7770410/working/building/REAL300020113883 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113883 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113883/0 /scratch/stefan/7770410/working/building/REAL300020113883 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1382) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1382 `/scratch/stefan/7770410/working/3D/1382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC=CC1=CC=CC=C1F)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113883.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113883 none O=C(CC=CC1=CC=CC=C1F)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 14, 22, 22, 47, 47, 32, 47, 47, 47, 1, 1, 1, 1, 1, 7, 7, 7, 21, 31, 31, 31, 31, 31, 7, 7, 1, 14, 14, 22, 22, 47, 47, 47, 47, 4, 1, 1, 1, 1, 7, 21, 21, 31, 31, 1, 1] 201 rigid atoms, others: [48, 38, 39, 40, 41, 12, 13, 14, 15, 16, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 309 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113883 none O=C(CC=CC1=CC=CC=C1F)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 58, 68, 68, 113, 113, 99, 113, 113, 113, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 58, 58, 68, 68, 113, 113, 113, 113, 14, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 426 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113883 none O=C(CC=CC1=CC=CC=C1F)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 47, 47, 47, 113, 113, 113, 162, 201, 201, 201, 201, 201, 113, 113, 47, 15, 15, 7, 7, 1, 1, 1, 1, 32, 47, 47, 47, 47, 113, 162, 162, 201, 201, 47, 47] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 36] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 746 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113883 none O=C(CC=CC1=CC=CC=C1F)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 138, 154, 154, 201, 201, 201, 201, 201, 201, 31, 31, 31, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 31, 138, 138, 154, 154, 201, 201, 201, 201, 42, 31, 31, 31, 31, 9, 4, 4, 2, 2, 31, 31] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 661 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113883 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113883/1 /scratch/stefan/7770410/working/building/REAL300020113883 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1383) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1383 `/scratch/stefan/7770410/working/3D/1383' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC=CC1=CC=CC=C1F)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113883.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113883/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113883 none O=C(CC=CC1=CC=CC=C1F)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 14, 22, 22, 47, 47, 32, 47, 47, 47, 1, 1, 1, 1, 1, 7, 7, 7, 21, 31, 31, 31, 31, 31, 7, 7, 1, 14, 14, 22, 22, 47, 47, 47, 47, 4, 1, 1, 1, 1, 7, 21, 21, 31, 31, 1, 1] 201 rigid atoms, others: [48, 38, 39, 40, 41, 12, 13, 14, 15, 16, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 309 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113883 none O=C(CC=CC1=CC=CC=C1F)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 58, 68, 68, 113, 113, 99, 113, 113, 113, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 58, 58, 68, 68, 113, 113, 113, 113, 14, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 426 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113883 none O=C(CC=CC1=CC=CC=C1F)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 47, 47, 47, 113, 113, 113, 161, 201, 201, 201, 201, 201, 113, 113, 47, 15, 15, 7, 7, 1, 1, 1, 1, 32, 47, 47, 47, 47, 113, 161, 161, 201, 201, 47, 47] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 36] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 743 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113883 none O=C(CC=CC1=CC=CC=C1F)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 137, 153, 153, 201, 201, 201, 201, 201, 201, 31, 31, 31, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 31, 137, 137, 153, 153, 201, 201, 201, 201, 42, 31, 31, 31, 31, 9, 4, 4, 2, 2, 31, 31] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 657 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113883 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113883 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113883/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113883/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113883 Building REAL300020113884 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113884' /scratch/stefan/7770410/working/building/REAL300020113884 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113884 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113884/0 /scratch/stefan/7770410/working/building/REAL300020113884 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1384) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1384 `/scratch/stefan/7770410/working/3D/1384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC=CC1=CC=C(F)C=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113884.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113884 none O=C(CC=CC1=CC=C(F)C=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 22, 39, 39, 52, 52, 52, 52, 52, 52, 1, 1, 1, 1, 1, 7, 7, 7, 19, 31, 31, 31, 31, 31, 7, 7, 1, 22, 22, 39, 39, 52, 52, 52, 52, 5, 1, 1, 1, 1, 7, 19, 19, 31, 31, 1, 1] 201 rigid atoms, others: [48, 38, 39, 40, 41, 12, 13, 14, 15, 16, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 280 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113884 none O=C(CC=CC1=CC=C(F)C=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 83, 114, 114, 130, 130, 130, 130, 130, 130, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 83, 83, 114, 114, 130, 130, 130, 130, 16, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 450 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113884 none O=C(CC=CC1=CC=C(F)C=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 10, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 52, 52, 52, 130, 130, 130, 167, 201, 201, 201, 201, 201, 130, 130, 52, 10, 10, 3, 3, 1, 1, 1, 1, 31, 52, 52, 52, 52, 130, 167, 167, 201, 201, 52, 52] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 36] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 679 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113884 none O=C(CC=CC1=CC=C(F)C=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 183, 201, 201, 201, 201, 201, 201, 201, 201, 35, 35, 35, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 35, 183, 183, 201, 201, 201, 201, 201, 201, 51, 35, 35, 35, 35, 9, 4, 4, 2, 2, 35, 35] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 729 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113884 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113884/1 /scratch/stefan/7770410/working/building/REAL300020113884 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1385) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1385 `/scratch/stefan/7770410/working/3D/1385' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC=CC1=CC=C(F)C=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113884.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113884 none O=C(CC=CC1=CC=C(F)C=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 22, 39, 39, 52, 52, 52, 52, 52, 52, 1, 1, 1, 1, 1, 7, 7, 7, 19, 31, 31, 31, 31, 31, 7, 7, 1, 22, 22, 39, 39, 52, 52, 52, 52, 5, 1, 1, 1, 1, 7, 19, 19, 31, 31, 1, 1] 201 rigid atoms, others: [48, 38, 39, 40, 41, 12, 13, 14, 15, 16, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 280 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113884 none O=C(CC=CC1=CC=C(F)C=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 83, 114, 114, 130, 130, 130, 130, 130, 130, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 83, 83, 114, 114, 130, 130, 130, 130, 16, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 450 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113884 none O=C(CC=CC1=CC=C(F)C=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 10, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 52, 52, 52, 130, 130, 130, 167, 201, 201, 201, 201, 201, 130, 130, 52, 10, 10, 3, 3, 1, 1, 1, 1, 31, 52, 52, 52, 52, 130, 167, 167, 201, 201, 52, 52] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 36] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 679 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113884 none O=C(CC=CC1=CC=C(F)C=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 183, 201, 201, 201, 201, 201, 201, 201, 201, 35, 35, 35, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 35, 183, 183, 201, 201, 201, 201, 201, 201, 51, 35, 35, 35, 35, 9, 4, 4, 2, 2, 35, 35] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 729 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113884 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113884 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113884/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113884/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113884 Building REAL300020113885 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113885' /scratch/stefan/7770410/working/building/REAL300020113885 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113885 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113885/0 /scratch/stefan/7770410/working/building/REAL300020113885 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1386) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1386 `/scratch/stefan/7770410/working/3D/1386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2CCCCCN12) `REAL300020113885.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113885 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2CCCCCN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 12, 46, 109, 109, 109, 109, 109, 109, 109, 109, 109, 46, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 109, 109, 109, 109, 109, 109, 109, 109, 109, 109, 109] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 251 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113885 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2CCCCCN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 85, 85, 85, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 85, 158, 201, 201, 201, 201, 201, 201, 201, 201, 201, 158, 85, 85, 85, 85, 14, 6, 6, 4, 4, 85, 85, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 524 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113885 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2CCCCCN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 51, 69, 85, 85, 85, 85, 12, 12, 1, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 12, 51, 51, 69, 69, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 333 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113885 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2CCCCCN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 22, 22, 22, 109, 109, 109, 171, 201, 201, 201, 201, 201, 109, 109, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 22, 22, 22, 22, 109, 171, 171, 201, 201, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 681 number of broken/clashed sets: 201 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113885 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113885/1 /scratch/stefan/7770410/working/building/REAL300020113885 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1387) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1387 `/scratch/stefan/7770410/working/3D/1387' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2CCCCCN12) `REAL300020113885.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113885/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113885 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2CCCCCN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 12, 46, 109, 109, 109, 109, 109, 109, 109, 109, 109, 46, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 109, 109, 109, 109, 109, 109, 109, 109, 109, 109, 109] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 251 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113885 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2CCCCCN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 85, 85, 85, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 85, 158, 201, 201, 201, 201, 201, 201, 201, 201, 201, 158, 85, 85, 85, 85, 14, 6, 6, 4, 4, 85, 85, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 524 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113885 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2CCCCCN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 51, 69, 85, 85, 85, 85, 12, 12, 1, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 12, 51, 51, 69, 69, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 333 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113885 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2CCCCCN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 5, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 22, 22, 22, 109, 109, 109, 171, 201, 201, 201, 201, 201, 109, 109, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 22, 22, 22, 22, 109, 171, 171, 201, 201, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 681 number of broken/clashed sets: 201 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113885 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113885 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113885/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113885/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113885 Building REAL300020113886 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113886' /scratch/stefan/7770410/working/building/REAL300020113886 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113886 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113886/0 /scratch/stefan/7770410/working/building/REAL300020113886 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1388) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1388 `/scratch/stefan/7770410/working/3D/1388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=NC=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113886.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113886 none COC1=CC=NC=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 26, 27, 27, 27, 27, 27, 24, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 29, 42, 42, 42, 42, 42, 11, 11, 1, 29, 29, 29, 27, 27, 27, 24, 24, 6, 1, 1, 1, 1, 11, 29, 29, 42, 42, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 259 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113886 none COC1=CC=NC=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [122, 115, 117, 117, 117, 117, 117, 110, 33, 33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 11, 122, 122, 122, 117, 117, 117, 110, 110, 33, 11, 11, 11, 11, 1, 5, 5, 7, 7, 11, 11] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 447 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113886 none COC1=CC=NC=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 27, 27, 27, 117, 117, 117, 172, 201, 201, 201, 201, 201, 117, 117, 27, 4, 4, 4, 1, 1, 1, 5, 5, 12, 27, 27, 27, 27, 117, 172, 172, 201, 201, 27, 27] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 33, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 659 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113886 none COC1=CC=NC=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 194, 98, 98, 98, 42, 42, 42, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 42, 201, 201, 201, 201, 201, 201, 194, 194, 98, 42, 42, 42, 42, 7, 4, 4, 2, 2, 42, 42] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 740 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113886 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113886/1 /scratch/stefan/7770410/working/building/REAL300020113886 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1389) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1389 `/scratch/stefan/7770410/working/3D/1389' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=NC=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113886.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113886 none COC1=CC=NC=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 26, 27, 27, 27, 27, 27, 24, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 29, 42, 42, 42, 42, 42, 11, 11, 1, 29, 29, 29, 27, 27, 27, 24, 24, 6, 1, 1, 1, 1, 11, 29, 29, 42, 42, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 259 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113886 none COC1=CC=NC=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [122, 115, 117, 117, 117, 117, 117, 110, 33, 33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 11, 122, 122, 122, 117, 117, 117, 110, 110, 33, 11, 11, 11, 11, 1, 5, 5, 7, 7, 11, 11] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 447 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113886 none COC1=CC=NC=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 27, 27, 27, 117, 117, 117, 172, 201, 201, 201, 201, 201, 117, 117, 27, 4, 4, 4, 1, 1, 1, 5, 5, 12, 27, 27, 27, 27, 117, 172, 172, 201, 201, 27, 27] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 33, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 659 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113886 none COC1=CC=NC=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 194, 98, 98, 98, 42, 42, 42, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 42, 201, 201, 201, 201, 201, 201, 194, 194, 98, 42, 42, 42, 42, 7, 4, 4, 2, 2, 42, 42] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 740 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113886 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113886 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113886/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113886/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113886 Building REAL300020113887 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113887' /scratch/stefan/7770410/working/building/REAL300020113887 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113887 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113887/0 /scratch/stefan/7770410/working/building/REAL300020113887 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1390) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1390 `/scratch/stefan/7770410/working/3D/1390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1C1CC1) `REAL300020113887.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113887 none CC1C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 28, 41, 41, 41, 41, 41, 8, 8, 1, 26, 26, 33, 33, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 8, 28, 28, 41, 41, 1, 1, 26, 33, 33, 33, 33, 33] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 42, 21, 41] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48]) total number of confs: 255 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113887 none CC1C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 15, 15, 15, 33, 33, 33, 100, 100, 100, 157, 201, 201, 201, 201, 201, 100, 100, 33, 1, 1, 1, 1, 3, 3, 3, 3, 3, 15, 33, 33, 33, 33, 100, 157, 157, 201, 201, 33, 33, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 48, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 740 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113887 none CC1C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 20, 20, 20, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 89, 89, 100, 100, 89, 89, 89, 89, 89, 20, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 89, 100, 100, 100, 100, 100] 201 rigid atoms, others: [36, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 299 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113887 none CC1C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 11, 11, 11, 26, 26, 26, 89, 89, 89, 152, 200, 200, 200, 200, 200, 89, 89, 26, 1, 1, 3, 3, 1, 1, 1, 1, 1, 11, 26, 26, 26, 26, 89, 152, 152, 200, 200, 26, 26, 1, 3, 3, 3, 3, 3] 201 rigid atoms, others: [0, 1, 2, 3, 43, 22, 23, 26, 27, 28, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 757 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113887 none CC1C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 68, 68, 68, 42, 42, 42, 9, 9, 9, 5, 2, 1, 1, 1, 1, 1, 1, 9, 9, 42, 200, 200, 201, 201, 200, 200, 200, 200, 200, 68, 42, 42, 42, 42, 9, 5, 5, 2, 2, 42, 42, 200, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 567 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113887 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113887/1 /scratch/stefan/7770410/working/building/REAL300020113887 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1391) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1391 `/scratch/stefan/7770410/working/3D/1391' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1C1CC1) `REAL300020113887.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113887 none CC1C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 29, 42, 42, 42, 42, 42, 9, 9, 1, 26, 26, 33, 33, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 9, 29, 29, 42, 42, 1, 1, 26, 33, 33, 33, 33, 33] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 42, 21, 41] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48]) total number of confs: 256 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113887 none CC1C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 15, 15, 15, 33, 33, 33, 101, 101, 101, 157, 201, 201, 201, 201, 201, 101, 101, 33, 1, 1, 1, 1, 3, 3, 3, 3, 3, 15, 33, 33, 33, 33, 101, 157, 157, 201, 201, 33, 33, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 48, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 736 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113887 none CC1C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 22, 22, 22, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 9, 90, 90, 101, 101, 90, 90, 90, 90, 90, 22, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 90, 101, 101, 101, 101, 101] 201 rigid atoms, others: [36, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 301 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113887 none CC1C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 11, 11, 11, 26, 26, 26, 90, 90, 90, 152, 200, 200, 200, 200, 200, 90, 90, 26, 1, 1, 3, 3, 1, 1, 1, 1, 1, 11, 26, 26, 26, 26, 90, 152, 152, 200, 200, 26, 26, 1, 3, 3, 3, 3, 3] 201 rigid atoms, others: [0, 1, 2, 3, 43, 22, 23, 26, 27, 28, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 753 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113887 none CC1C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 69, 69, 69, 43, 43, 43, 9, 9, 9, 5, 2, 1, 1, 1, 1, 1, 1, 9, 9, 43, 200, 200, 201, 201, 200, 200, 200, 200, 200, 69, 43, 43, 43, 43, 9, 5, 5, 2, 2, 43, 43, 200, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 567 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113887 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113887 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113887/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113887/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113887 Building REAL300020113888 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113888' /scratch/stefan/7770410/working/building/REAL300020113888 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113888 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113888/0 /scratch/stefan/7770410/working/building/REAL300020113888 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1392) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1392 `/scratch/stefan/7770410/working/3D/1392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=NC(C(C)(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020113888.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113888 none CC1=CC=NC(C(C)(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 25, 18, 6, 18, 18, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 37, 53, 60, 60, 60, 60, 11, 11, 1, 25, 25, 25, 25, 25, 25, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 11, 37, 37, 53, 53, 1, 1, 25] 201 rigid atoms, others: [43, 41, 42, 11, 12, 13, 14, 15, 50, 51, 27, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 52]) total number of confs: 301 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113888 none CC1=CC=NC(C(C)(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 101, 101, 84, 40, 84, 84, 40, 40, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 11, 11, 11, 11, 1, 1, 11, 101, 101, 101, 101, 101, 101, 84, 84, 84, 84, 84, 84, 40, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 101] 201 rigid atoms, others: [45, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 398 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113888 none CC1=CC=NC(C(C)(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 25, 25, 25, 101, 101, 101, 167, 201, 201, 201, 201, 201, 101, 101, 25, 1, 2, 2, 2, 1, 1, 5, 5, 5, 5, 5, 5, 9, 25, 25, 25, 25, 101, 167, 167, 201, 201, 25, 25, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 52, 28, 5] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 718 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113888 none CC1=CC=NC(C(C)(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 131, 201, 201, 131, 131, 60, 60, 60, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 60, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 131, 60, 60, 60, 60, 11, 6, 6, 4, 4, 60, 60, 201] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 761 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113888 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113888/1 /scratch/stefan/7770410/working/building/REAL300020113888 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1393) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1393 `/scratch/stefan/7770410/working/3D/1393' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=NC(C(C)(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020113888.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113888 none CC1=CC=NC(C(C)(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 25, 18, 6, 18, 18, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 37, 53, 61, 61, 61, 61, 11, 11, 1, 25, 25, 25, 25, 25, 25, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 11, 37, 37, 53, 53, 1, 1, 25] 201 rigid atoms, others: [43, 41, 42, 11, 12, 13, 14, 15, 50, 51, 27, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 52]) total number of confs: 303 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113888 none CC1=CC=NC(C(C)(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 101, 101, 84, 40, 84, 84, 40, 40, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 11, 11, 11, 11, 1, 1, 11, 101, 101, 101, 101, 101, 101, 84, 84, 84, 84, 84, 84, 40, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 101] 201 rigid atoms, others: [45, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 398 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113888 none CC1=CC=NC(C(C)(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 25, 25, 25, 101, 101, 101, 166, 201, 201, 201, 201, 201, 101, 101, 25, 1, 2, 2, 2, 1, 1, 5, 5, 5, 5, 5, 5, 9, 25, 25, 25, 25, 101, 166, 166, 201, 201, 25, 25, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 52, 28, 5] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 718 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113888 none CC1=CC=NC(C(C)(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 130, 201, 201, 130, 130, 60, 60, 60, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 60, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 130, 60, 60, 60, 60, 11, 6, 6, 4, 4, 60, 60, 201] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 763 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113888 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113888 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113888/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113888/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113888 Building REAL300020113889 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113889' /scratch/stefan/7770410/working/building/REAL300020113889 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113889 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113889/0 /scratch/stefan/7770410/working/building/REAL300020113889 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1394) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1394 `/scratch/stefan/7770410/working/3D/1394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2CCCC[N@@H+]21) `REAL300020113889.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113889 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2CCCC[N@@H+]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 8, 8, 8, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 8, 20, 21, 21, 21, 21, 21, 21, 21, 21, 21, 20, 8, 8, 8, 8, 1, 4, 4, 4, 4, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 22 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 71 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113889 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2CCCC[N@@H+]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 9, 9, 9, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 21, 22, 22, 22, 22, 22, 22, 22, 22, 22, 21, 9, 9, 9, 9, 4, 3, 3, 1, 1, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 22 rigid atoms, others: [37, 38, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 68 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113889 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2CCCC[N@@H+]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 9, 9, 9, 9, 9, 9, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 1, 1, 1, 8, 9, 9, 9, 9, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 22 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 31 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113889 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2CCCC[N@@H+]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 7, 21, 21, 21, 22, 22, 22, 22, 22, 22, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 7, 7, 7, 21, 22, 22, 22, 22, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 22 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 41 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113889 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113889/1 /scratch/stefan/7770410/working/building/REAL300020113889 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1395) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1395 `/scratch/stefan/7770410/working/3D/1395' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2CCCC[N@H+]21) `REAL300020113889.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113889 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2CCCC[N@H+]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 13, 13, 13, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 13, 55, 125, 125, 125, 125, 125, 125, 125, 125, 125, 55, 13, 13, 13, 13, 1, 5, 5, 5, 5, 13, 13, 125, 125, 125, 125, 125, 125, 125, 125, 125, 125, 125, 125, 125, 125] 151 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 366 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113889 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2CCCC[N@H+]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 28, 28, 28, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 28, 93, 151, 151, 151, 151, 151, 151, 151, 151, 151, 93, 28, 28, 28, 28, 5, 3, 3, 1, 1, 28, 28, 151, 151, 151, 151, 151, 151, 151, 151, 151, 151, 151, 151, 151, 151] 151 rigid atoms, others: [37, 38, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 436 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113889 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2CCCC[N@H+]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 28, 28, 28, 28, 28, 28, 13, 13, 1, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 1, 1, 1, 1, 13, 28, 28, 28, 28, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 151 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113889 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2CCCC[N@H+]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 31, 31, 31, 125, 125, 125, 151, 151, 151, 151, 151, 151, 125, 125, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 31, 31, 31, 31, 125, 151, 151, 151, 151, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 151 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 350 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113889 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113889 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113889/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113889/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113889 Building REAL300020113890 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113890' /scratch/stefan/7770410/working/building/REAL300020113890 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113890 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113890/0 /scratch/stefan/7770410/working/building/REAL300020113890 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1396) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1396 `/scratch/stefan/7770410/working/3D/1396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NC=C1) `REAL300020113890.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113890 none CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 73, 23, 23, 23, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 73, 73, 23, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 94, 94, 94, 94] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 409 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113890 none CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 172, 65, 65, 65, 38, 38, 38, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 38, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 172, 172, 65, 38, 38, 38, 38, 8, 4, 4, 2, 2, 38, 38, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 807 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113890 none CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 21, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 26, 38, 38, 38, 38, 38, 8, 8, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 21, 21, 6, 1, 1, 1, 1, 8, 26, 26, 38, 38, 1, 1, 29, 29, 29, 29] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 44, 45, 21, 38, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47, 48, 49]) total number of confs: 270 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113890 none CC(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 5, 14, 14, 14, 29, 29, 29, 94, 94, 94, 151, 201, 201, 201, 201, 201, 94, 94, 29, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 5, 5, 14, 29, 29, 29, 29, 94, 151, 151, 201, 201, 29, 29, 1, 1, 1, 1] 201 rigid atoms, others: [1, 46, 47, 48, 49, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 782 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113890 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113890/1 /scratch/stefan/7770410/working/building/REAL300020113890 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1397) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1397 `/scratch/stefan/7770410/working/3D/1397' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NC=C1) `REAL300020113890.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113890 none CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 72, 23, 23, 23, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 72, 72, 23, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 93, 93, 93, 93] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 406 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113890 none CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 172, 65, 65, 65, 38, 38, 38, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 38, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 172, 172, 65, 38, 38, 38, 38, 8, 4, 4, 2, 2, 38, 38, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 807 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113890 none CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 21, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 26, 38, 38, 38, 38, 38, 8, 8, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 21, 21, 6, 1, 1, 1, 1, 8, 26, 26, 38, 38, 1, 1, 29, 29, 29, 29] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 44, 45, 21, 38, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47, 48, 49]) total number of confs: 270 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113890 none CC(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 5, 14, 14, 14, 29, 29, 29, 93, 93, 93, 151, 201, 201, 201, 201, 201, 93, 93, 29, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 5, 5, 14, 29, 29, 29, 29, 93, 151, 151, 201, 201, 29, 29, 1, 1, 1, 1] 201 rigid atoms, others: [1, 46, 47, 48, 49, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 784 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113890 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113890 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113890/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113890/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113890 Building REAL300020113891 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113891' /scratch/stefan/7770410/working/building/REAL300020113891 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113891 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113891/0 /scratch/stefan/7770410/working/building/REAL300020113891 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1398) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1398 `/scratch/stefan/7770410/working/3D/1398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCNC(=O)C1) `REAL300020113891.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113891 none CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 48, 66, 72, 72, 72, 72, 12, 12, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 1, 1, 1, 1, 12, 48, 48, 66, 66, 1, 1, 10, 10, 10, 10, 10, 10, 10] 201 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 41, 40, 20, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 299 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113891 none CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 52, 52, 52, 12, 12, 12, 1, 1, 1, 1, 1, 9, 12, 15, 15, 15, 15, 1, 1, 12, 68, 68, 68, 68, 68, 68, 68, 68, 68, 52, 12, 12, 12, 12, 1, 9, 9, 12, 12, 12, 12, 68, 68, 68, 68, 68, 68, 68] 201 rigid atoms, others: [35, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 240 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113891 none CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 10, 10, 10, 68, 68, 68, 160, 201, 201, 201, 201, 201, 68, 68, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 10, 10, 10, 10, 68, 160, 160, 201, 201, 10, 10, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 42, 43, 44, 45, 46, 47, 48, 21, 22, 23, 24, 25, 26] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 779 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113891 none CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 179, 179, 179, 73, 73, 73, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 73, 201, 201, 201, 201, 201, 201, 201, 201, 201, 179, 73, 73, 73, 73, 17, 6, 6, 4, 4, 73, 73, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 557 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113891 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113891/1 /scratch/stefan/7770410/working/building/REAL300020113891 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1399) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1399 `/scratch/stefan/7770410/working/3D/1399' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCNC(=O)C1) `REAL300020113891.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113891 none CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 49, 67, 73, 73, 73, 73, 12, 12, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 1, 1, 1, 1, 12, 49, 49, 67, 67, 1, 1, 10, 10, 10, 10, 10, 10, 10] 201 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 41, 40, 20, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 305 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113891 none CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 53, 53, 53, 12, 12, 12, 1, 1, 1, 1, 1, 9, 12, 15, 15, 15, 15, 1, 1, 12, 68, 68, 68, 68, 68, 68, 68, 68, 68, 53, 12, 12, 12, 12, 1, 9, 9, 12, 12, 12, 12, 68, 68, 68, 68, 68, 68, 68] 201 rigid atoms, others: [35, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 240 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113891 none CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 10, 10, 10, 68, 68, 68, 160, 201, 201, 201, 201, 201, 68, 68, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 10, 10, 10, 10, 68, 160, 160, 201, 201, 10, 10, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 42, 43, 44, 45, 46, 47, 48, 21, 22, 23, 24, 25, 26] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 778 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113891 none CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 179, 179, 179, 73, 73, 73, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 73, 201, 201, 201, 201, 201, 201, 201, 201, 201, 179, 73, 73, 73, 73, 17, 6, 6, 4, 4, 73, 73, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 557 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113891 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113891 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113891/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113891/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113891 Building REAL300020113892 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113892' /scratch/stefan/7770410/working/building/REAL300020113892 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113892 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113892/0 /scratch/stefan/7770410/working/building/REAL300020113892 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1400) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1400 `/scratch/stefan/7770410/working/3D/1400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC12CC2) `REAL300020113892.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113892 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC12CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 11 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 40 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113892 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC12CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 8, 8, 8, 6, 6, 6, 4, 2, 1, 1, 1, 1, 1, 1, 6, 6, 8, 11, 11, 11, 11, 11, 11, 11, 11, 8, 8, 8, 8, 6, 4, 4, 2, 2, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 11 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 40 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113892 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC12CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 6, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 11 rigid atoms, others: [2, 3, 4, 5, 6, 18, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113892 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC12CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 7, 7, 7, 9, 9, 9, 11, 11, 11, 11, 11, 11, 9, 9, 7, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 9, 11, 11, 11, 11, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 11 rigid atoms, others: [1, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 32 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113892 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113892/1 /scratch/stefan/7770410/working/building/REAL300020113892 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1401) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1401 `/scratch/stefan/7770410/working/3D/1401' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC12CC2) `REAL300020113892.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113892 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC12CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 11 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 40 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113892 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC12CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 8, 8, 8, 6, 6, 6, 4, 2, 1, 1, 1, 1, 1, 1, 6, 6, 8, 11, 11, 11, 11, 11, 11, 11, 11, 8, 8, 8, 8, 6, 4, 4, 2, 2, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 11 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 40 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113892 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC12CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 6, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 11 rigid atoms, others: [2, 3, 4, 5, 6, 18, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113892 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC12CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 7, 7, 7, 9, 9, 9, 11, 11, 11, 11, 11, 11, 9, 9, 7, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 9, 11, 11, 11, 11, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 11 rigid atoms, others: [1, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 32 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113892 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113892 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113892/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113892/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113892 Building REAL300020113893 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113893' /scratch/stefan/7770410/working/building/REAL300020113893 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113893 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113893/0 /scratch/stefan/7770410/working/building/REAL300020113893 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1402) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1402 `/scratch/stefan/7770410/working/3D/1402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COCC1=CC(=O)NC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113893.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113893 none O=C(COCC1=CC(=O)NC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 1, 1, 1, 11, 8, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 19, 24, 45, 76, 76, 76, 76, 76, 76, 1, 1, 1, 1, 1, 7, 7, 7, 15, 24, 24, 24, 24, 24, 7, 7, 1, 19, 19, 45, 45, 76, 76, 76, 76, 5, 1, 1, 1, 1, 7, 15, 15, 24, 24, 1, 1] 201 rigid atoms, others: [48, 38, 39, 40, 41, 12, 13, 14, 15, 16, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 324 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113893 none O=C(COCC1=CC(=O)NC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 1, 1, 1, 11, 8, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 61, 65, 118, 159, 159, 159, 159, 159, 159, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 61, 61, 118, 118, 156, 159, 159, 159, 17, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 603 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113893 none O=C(COCC1=CC(=O)NC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 1, 1, 1, 11, 8, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 42, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 76, 76, 76, 159, 159, 159, 186, 201, 201, 201, 201, 201, 159, 159, 76, 42, 42, 7, 7, 1, 1, 1, 1, 53, 76, 76, 76, 76, 159, 186, 186, 201, 201, 76, 76] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 36] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 626 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113893 none O=C(COCC1=CC(=O)NC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 1, 1, 1, 11, 8, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 84, 98, 153, 201, 201, 201, 201, 201, 201, 24, 24, 24, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 24, 84, 84, 153, 153, 201, 201, 201, 201, 30, 24, 24, 24, 24, 7, 4, 4, 2, 2, 24, 24] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 726 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113893 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113893/1 /scratch/stefan/7770410/working/building/REAL300020113893 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1403) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1403 `/scratch/stefan/7770410/working/3D/1403' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COCC1=CC(=O)NC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113893.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113893 none O=C(COCC1=CC(=O)NC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 1, 1, 1, 11, 8, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 19, 25, 46, 79, 79, 79, 79, 79, 79, 1, 1, 1, 1, 1, 7, 7, 7, 15, 24, 24, 24, 24, 24, 7, 7, 1, 19, 19, 46, 46, 79, 79, 79, 79, 5, 1, 1, 1, 1, 7, 15, 15, 24, 24, 1, 1] 201 rigid atoms, others: [48, 38, 39, 40, 41, 12, 13, 14, 15, 16, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 328 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113893 none O=C(COCC1=CC(=O)NC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 1, 1, 1, 11, 8, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 61, 67, 119, 162, 162, 162, 162, 162, 162, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 61, 61, 119, 119, 159, 162, 162, 162, 17, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 608 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113893 none O=C(COCC1=CC(=O)NC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 1, 1, 1, 11, 8, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 44, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 79, 79, 79, 162, 162, 162, 186, 201, 201, 201, 201, 201, 162, 162, 79, 44, 44, 7, 7, 1, 1, 1, 1, 55, 79, 79, 79, 79, 162, 186, 186, 201, 201, 79, 79] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 36] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 615 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113893 none O=C(COCC1=CC(=O)NC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 1, 1, 1, 11, 8, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 84, 98, 153, 201, 201, 201, 201, 201, 201, 24, 24, 24, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 24, 84, 84, 153, 153, 201, 201, 201, 201, 30, 24, 24, 24, 24, 7, 4, 4, 2, 2, 24, 24] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 726 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113893 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113893 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113893/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113893/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113893 Building REAL300020113894 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113894' /scratch/stefan/7770410/working/building/REAL300020113894 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113894 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113894/0 /scratch/stefan/7770410/working/building/REAL300020113894 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1404) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1404 `/scratch/stefan/7770410/working/3D/1404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)N=C2C=C1) `REAL300020113894.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113894 none CC1=CN2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)N=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 70, 93, 117, 117, 117, 117, 13, 13, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 13, 70, 70, 93, 93, 1, 1, 17, 17] 201 rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 11, 12, 45, 44, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47]) total number of confs: 432 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113894 none CC1=CN2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)N=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 89, 89, 54, 54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 21, 21, 21, 21, 1, 1, 13, 89, 89, 89, 89, 89, 89, 89, 89, 89, 54, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 89, 89] 201 rigid atoms, others: [39, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 260 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113894 none CC1=CN2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)N=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 89, 89, 89, 166, 201, 201, 201, 201, 201, 89, 89, 17, 1, 1, 1, 1, 2, 2, 2, 1, 1, 5, 17, 17, 17, 17, 89, 166, 166, 201, 201, 17, 17, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 46, 47, 33, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 706 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113894 none CC1=CN2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)N=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 187, 187, 187, 118, 118, 118, 23, 23, 23, 6, 4, 1, 1, 1, 1, 1, 1, 23, 23, 118, 201, 201, 201, 201, 201, 201, 201, 201, 201, 187, 118, 118, 118, 118, 23, 6, 6, 4, 4, 118, 118, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 527 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113894 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113894/1 /scratch/stefan/7770410/working/building/REAL300020113894 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1405) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1405 `/scratch/stefan/7770410/working/3D/1405' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)N=C2C=C1) `REAL300020113894.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113894/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113894 none CC1=CN2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)N=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 70, 93, 117, 117, 117, 117, 13, 13, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 13, 70, 70, 93, 93, 1, 1, 17, 17] 201 rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 11, 12, 45, 44, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47]) total number of confs: 432 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113894 none CC1=CN2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)N=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 89, 89, 54, 54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 21, 21, 21, 21, 1, 1, 13, 89, 89, 89, 89, 89, 89, 89, 89, 89, 54, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 89, 89] 201 rigid atoms, others: [39, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 260 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113894 none CC1=CN2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)N=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 89, 89, 89, 166, 201, 201, 201, 201, 201, 89, 89, 17, 1, 1, 1, 1, 2, 2, 2, 1, 1, 5, 17, 17, 17, 17, 89, 166, 166, 201, 201, 17, 17, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 46, 47, 33, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 706 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113894 none CC1=CN2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)N=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 187, 187, 187, 118, 118, 118, 23, 23, 23, 6, 4, 1, 1, 1, 1, 1, 1, 23, 23, 118, 201, 201, 201, 201, 201, 201, 201, 201, 201, 187, 118, 118, 118, 118, 23, 6, 6, 4, 4, 118, 118, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 527 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113894 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113894 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113894/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113894/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113894 Building REAL300020113895 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113895' /scratch/stefan/7770410/working/building/REAL300020113895 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113895 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113895/0 /scratch/stefan/7770410/working/building/REAL300020113895 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1406) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1406 `/scratch/stefan/7770410/working/3D/1406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCN2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)N=C2C1) `REAL300020113895.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113895 none CC1CCN2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)N=C2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 56, 79, 96, 96, 96, 96, 13, 13, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 56, 56, 79, 79, 1, 1, 16, 16] 201 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 48, 49, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50, 51]) total number of confs: 378 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113895 none CC1CCN2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)N=C2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 83, 83, 83, 56, 56, 56, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 13, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 56, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13, 83, 83] 201 rigid atoms, others: [43, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 236 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113895 none CC1CCN2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)N=C2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 16, 16, 16, 83, 83, 83, 168, 201, 201, 201, 201, 201, 83, 83, 16, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 16, 16, 16, 16, 83, 168, 168, 201, 201, 16, 16, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 34, 50, 35, 51, 36, 26, 27, 28, 37, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 733 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113895 none CC1CCN2C=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)N=C2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 96, 96, 96, 16, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 96, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 96, 96, 96, 96, 16, 6, 6, 4, 4, 96, 96, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 554 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113895 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113895/1 /scratch/stefan/7770410/working/building/REAL300020113895 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1407) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1407 `/scratch/stefan/7770410/working/3D/1407' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCN2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)N=C2C1) `REAL300020113895.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113895/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113895 none CC1CCN2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)N=C2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 57, 80, 97, 97, 97, 97, 13, 13, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 57, 57, 80, 80, 1, 1, 16, 16] 201 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 48, 49, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50, 51]) total number of confs: 381 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113895 none CC1CCN2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)N=C2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 82, 82, 82, 56, 56, 56, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 13, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 56, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13, 82, 82] 201 rigid atoms, others: [43, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 234 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113895 none CC1CCN2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)N=C2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 16, 16, 16, 82, 82, 82, 168, 201, 201, 201, 201, 201, 82, 82, 16, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 16, 16, 16, 16, 82, 168, 168, 201, 201, 16, 16, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 34, 50, 35, 51, 36, 26, 27, 28, 37, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 735 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113895 none CC1CCN2C=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)N=C2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 97, 97, 97, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 97, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 97, 97, 97, 97, 15, 6, 6, 4, 4, 97, 97, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 555 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113895 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113895 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113895/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113895/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113895 Building REAL300020113896 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113896' /scratch/stefan/7770410/working/building/REAL300020113896 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113896 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113896/0 /scratch/stefan/7770410/working/building/REAL300020113896 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1408) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1408 `/scratch/stefan/7770410/working/3D/1408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(C(F)F)=NC=N1) `REAL300020113896.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113896 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(C(F)F)=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 15, 15, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 13, 61, 101, 101, 101, 147, 147, 101, 101, 101, 61, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 101, 147, 101] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 512 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113896 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(C(F)F)=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 15, 15, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [150, 150, 41, 41, 41, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 41, 150, 201, 201, 201, 201, 201, 201, 201, 201, 150, 41, 41, 41, 41, 8, 4, 4, 2, 2, 41, 41, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 477 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113896 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(C(F)F)=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 15, 15, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 29, 42, 42, 42, 42, 42, 13, 13, 1, 6, 15, 15, 15, 45, 45, 15, 15, 15, 6, 1, 1, 1, 1, 13, 29, 29, 42, 42, 1, 1, 15, 45, 15] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 319 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113896 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(C(F)F)=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 15, 15, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 15, 15, 15, 101, 101, 101, 154, 201, 201, 201, 201, 201, 101, 101, 15, 1, 1, 1, 1, 9, 9, 1, 1, 1, 4, 15, 15, 15, 15, 101, 154, 154, 201, 201, 15, 15, 1, 9, 1] 201 rigid atoms, others: [1, 40, 42, 19, 20, 21, 22, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41]) total number of confs: 740 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113896 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113896/1 /scratch/stefan/7770410/working/building/REAL300020113896 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1409) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1409 `/scratch/stefan/7770410/working/3D/1409' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(C(F)F)=NC=N1) `REAL300020113896.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113896 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(C(F)F)=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 15, 15, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 13, 61, 103, 103, 103, 148, 148, 103, 103, 103, 61, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 103, 148, 103] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 510 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113896 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(C(F)F)=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 15, 15, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [150, 150, 41, 41, 41, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 41, 150, 201, 201, 201, 201, 201, 201, 201, 201, 150, 41, 41, 41, 41, 8, 4, 4, 2, 2, 41, 41, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 477 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113896 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(C(F)F)=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 15, 15, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 29, 42, 42, 42, 42, 42, 13, 13, 1, 6, 16, 16, 16, 46, 46, 16, 16, 16, 6, 1, 1, 1, 1, 13, 29, 29, 42, 42, 1, 1, 16, 46, 16] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 320 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113896 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(C(F)F)=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 15, 15, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 16, 16, 16, 103, 103, 103, 156, 201, 201, 201, 201, 201, 103, 103, 16, 1, 1, 1, 1, 9, 9, 1, 1, 1, 4, 16, 16, 16, 16, 103, 156, 156, 201, 201, 16, 16, 1, 9, 1] 201 rigid atoms, others: [1, 40, 42, 19, 20, 21, 22, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41]) total number of confs: 731 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113896 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113896 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113896/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113896/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113896 Building REAL300020113897 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113897' /scratch/stefan/7770410/working/building/REAL300020113897 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113897 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113897/0 /scratch/stefan/7770410/working/building/REAL300020113897 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1410) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1410 `/scratch/stefan/7770410/working/3D/1410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1=CSC=C1) `REAL300020113897.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113897 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1=CSC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 12, 12, 12, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 12, 38, 90, 90, 90, 90, 90, 149, 149, 149, 149, 38, 12, 12, 12, 12, 1, 5, 5, 7, 7, 12, 12, 90, 90, 149, 149, 149] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 394 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113897 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1=CSC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 5, 23, 23, 43, 43, 43, 149, 149, 149, 181, 201, 201, 201, 201, 201, 149, 149, 43, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 23, 43, 43, 43, 43, 149, 181, 181, 201, 201, 43, 43, 5, 5, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 22, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 532 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113897 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1=CSC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 31, 31, 31, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 31, 67, 120, 120, 120, 120, 120, 201, 201, 201, 201, 67, 31, 31, 31, 31, 7, 4, 4, 2, 2, 31, 31, 120, 120, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 524 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113897 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1=CSC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 25, 33, 33, 33, 33, 33, 12, 12, 1, 6, 23, 23, 23, 23, 23, 43, 43, 43, 43, 6, 1, 1, 1, 1, 12, 25, 25, 33, 33, 1, 1, 23, 23, 43, 43, 43] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113897 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1=CSC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 23, 23, 23, 90, 90, 90, 109, 122, 122, 122, 122, 122, 90, 90, 23, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 23, 23, 23, 23, 90, 109, 109, 122, 122, 23, 23, 1, 1, 5, 5, 5] 201 rigid atoms, others: [1, 41, 42, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 325 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113897 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113897/1 /scratch/stefan/7770410/working/building/REAL300020113897 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1411) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1411 `/scratch/stefan/7770410/working/3D/1411' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1=CSC=C1) `REAL300020113897.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113897 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1=CSC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 12, 12, 12, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 12, 39, 91, 91, 91, 91, 91, 150, 150, 150, 150, 39, 12, 12, 12, 12, 1, 5, 5, 7, 7, 12, 12, 91, 91, 150, 150, 150] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 396 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113897 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1=CSC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 5, 22, 22, 42, 42, 42, 150, 150, 150, 182, 201, 201, 201, 201, 201, 150, 150, 42, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 22, 42, 42, 42, 42, 150, 182, 182, 201, 201, 42, 42, 5, 5, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 22, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 526 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113897 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1=CSC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 32, 32, 32, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 32, 69, 123, 123, 123, 123, 123, 201, 201, 201, 201, 69, 32, 32, 32, 32, 8, 4, 4, 2, 2, 32, 32, 123, 123, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 526 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113897 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1=CSC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 25, 33, 33, 33, 33, 33, 12, 12, 1, 6, 24, 24, 24, 24, 24, 42, 42, 42, 42, 6, 1, 1, 1, 1, 12, 25, 25, 33, 33, 1, 1, 24, 24, 42, 42, 42] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113897 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1=CSC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 24, 24, 24, 91, 91, 91, 110, 123, 123, 123, 123, 123, 91, 91, 24, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 24, 24, 24, 24, 91, 110, 110, 123, 123, 24, 24, 1, 1, 5, 5, 5] 201 rigid atoms, others: [1, 41, 42, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 328 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113897 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113897 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113897/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113897/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113897 Building REAL300020113898 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113898' /scratch/stefan/7770410/working/building/REAL300020113898 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113898 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113898/0 /scratch/stefan/7770410/working/building/REAL300020113898 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1412) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1412 `/scratch/stefan/7770410/working/3D/1412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N2C=CSC2=N1) `REAL300020113898.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113898 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N2C=CSC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 14, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 32, 47, 50, 50, 50, 50, 11, 11, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 11, 32, 32, 47, 47, 1, 1, 18, 18] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 42, 21, 41] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44]) total number of confs: 224 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113898 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N2C=CSC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 14, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 37, 37, 37, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 96, 96, 96, 96, 96, 96, 96, 96, 96, 37, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 96, 96] 201 rigid atoms, others: [36, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 213 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113898 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N2C=CSC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 14, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 8, 8, 8, 18, 18, 18, 96, 96, 96, 160, 201, 201, 201, 201, 201, 96, 96, 18, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 18, 18, 18, 18, 96, 160, 160, 201, 201, 18, 18, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 43, 44, 22, 23, 24, 25, 26, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 732 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113898 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N2C=CSC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 14, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 107, 107, 107, 50, 50, 50, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 50, 201, 201, 201, 201, 201, 201, 201, 201, 201, 107, 50, 50, 50, 50, 10, 6, 6, 4, 4, 50, 50, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 443 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113898 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113898/1 /scratch/stefan/7770410/working/building/REAL300020113898 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1413) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1413 `/scratch/stefan/7770410/working/3D/1413' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N2C=CSC2=N1) `REAL300020113898.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113898 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N2C=CSC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 14, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 32, 47, 50, 50, 50, 50, 11, 11, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 11, 32, 32, 47, 47, 1, 1, 18, 18] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 42, 21, 41] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44]) total number of confs: 224 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113898 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N2C=CSC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 14, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 37, 37, 37, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 96, 96, 96, 96, 96, 96, 96, 96, 96, 37, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 96, 96] 201 rigid atoms, others: [36, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 213 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113898 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N2C=CSC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 14, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 8, 8, 8, 18, 18, 18, 96, 96, 96, 160, 201, 201, 201, 201, 201, 96, 96, 18, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 18, 18, 18, 18, 96, 160, 160, 201, 201, 18, 18, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 43, 44, 22, 23, 24, 25, 26, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 732 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113898 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N2C=CSC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 14, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 107, 107, 107, 50, 50, 50, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 50, 201, 201, 201, 201, 201, 201, 201, 201, 201, 107, 50, 50, 50, 50, 10, 6, 6, 4, 4, 50, 50, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 443 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113898 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113898 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113898/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113898/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113898 Building REAL300020113899 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113899' /scratch/stefan/7770410/working/building/REAL300020113899 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113899 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113899/0 /scratch/stefan/7770410/working/building/REAL300020113899 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1414) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1414 `/scratch/stefan/7770410/working/3D/1414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN2CCC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)CC2=N1) `REAL300020113899.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113899 none CC1=CN2CCC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)CC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 23, 23, 23, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 32, 48, 55, 55, 55, 55, 11, 11, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 11, 32, 32, 48, 48, 1, 1, 23, 23] 201 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 48, 49, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50, 51]) total number of confs: 263 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113899 none CC1=CN2CCC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)CC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 97, 97, 97, 97, 33, 33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 97, 97, 97, 97, 97, 97, 97, 97, 97, 97, 97, 97, 33, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 97, 97] 201 rigid atoms, others: [43, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 287 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113899 none CC1=CN2CCC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)CC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 23, 23, 23, 97, 97, 97, 158, 201, 201, 201, 201, 201, 97, 97, 23, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 23, 23, 23, 23, 97, 158, 158, 201, 201, 23, 23, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 50, 35, 51, 36, 33, 27, 28, 26, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 748 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113899 none CC1=CN2CCC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)CC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 106, 106, 106, 56, 56, 56, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 56, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 106, 56, 56, 56, 56, 12, 6, 6, 4, 4, 56, 56, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 578 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113899 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113899/1 /scratch/stefan/7770410/working/building/REAL300020113899 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1415) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1415 `/scratch/stefan/7770410/working/3D/1415' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN2CCC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)CC2=N1) `REAL300020113899.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113899 none CC1=CN2CCC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)CC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 23, 23, 23, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 32, 48, 55, 55, 55, 55, 11, 11, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 11, 32, 32, 48, 48, 1, 1, 23, 23] 201 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 48, 49, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50, 51]) total number of confs: 263 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113899 none CC1=CN2CCC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)CC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 96, 96, 96, 33, 33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 33, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 96, 96] 201 rigid atoms, others: [43, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 285 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113899 none CC1=CN2CCC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)CC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 23, 23, 23, 96, 96, 96, 158, 201, 201, 201, 201, 201, 96, 96, 23, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 23, 23, 23, 23, 96, 158, 158, 201, 201, 23, 23, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 50, 35, 51, 36, 33, 27, 28, 26, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 756 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113899 none CC1=CN2CCC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)CC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 105, 105, 105, 56, 56, 56, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 56, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 105, 56, 56, 56, 56, 12, 6, 6, 4, 4, 56, 56, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 580 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113899 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113899 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113899/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113899/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113899 Building REAL300020113900 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113900' /scratch/stefan/7770410/working/building/REAL300020113900 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113900 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113900/0 /scratch/stefan/7770410/working/building/REAL300020113900 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1416) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1416 `/scratch/stefan/7770410/working/3D/1416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1C) `REAL300020113900.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113900 none COC1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 17, 17, 17, 17, 17, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 26, 39, 40, 40, 40, 40, 8, 8, 1, 17, 17, 32, 32, 32, 17, 17, 5, 1, 1, 1, 1, 8, 26, 26, 39, 39, 1, 1, 17, 17, 17] 201 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 215 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113900 none COC1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 80, 80, 80, 80, 80, 22, 22, 22, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 80, 80, 110, 110, 110, 80, 80, 22, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 80, 80, 80] 201 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 225 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113900 none COC1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 17, 80, 80, 80, 154, 200, 201, 201, 201, 201, 80, 80, 17, 1, 1, 4, 4, 4, 1, 1, 7, 17, 17, 17, 17, 80, 154, 154, 200, 200, 17, 17, 2, 2, 2] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 26, 27, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 793 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113900 none COC1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 77, 77, 77, 42, 42, 42, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 42, 201, 201, 201, 201, 201, 201, 201, 77, 42, 42, 42, 42, 10, 5, 5, 3, 3, 42, 42, 201, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 389 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113900 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113900/1 /scratch/stefan/7770410/working/building/REAL300020113900 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1417) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1417 `/scratch/stefan/7770410/working/3D/1417' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1C) `REAL300020113900.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113900/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113900 none COC1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 17, 17, 17, 17, 17, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 26, 39, 40, 40, 40, 40, 8, 8, 1, 17, 17, 31, 31, 31, 17, 17, 5, 1, 1, 1, 1, 8, 26, 26, 39, 39, 1, 1, 17, 17, 17] 201 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 214 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113900 none COC1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 81, 81, 81, 81, 81, 23, 23, 23, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 81, 81, 110, 110, 110, 81, 81, 23, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 81, 81, 81] 201 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 225 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113900 none COC1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 17, 81, 81, 81, 154, 200, 201, 201, 201, 201, 81, 81, 17, 1, 1, 4, 4, 4, 1, 1, 7, 17, 17, 17, 17, 81, 154, 154, 200, 200, 17, 17, 2, 2, 2] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 26, 27, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 788 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113900 none COC1=CN=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 76, 76, 76, 40, 40, 40, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 40, 201, 201, 201, 201, 201, 201, 201, 76, 40, 40, 40, 40, 9, 5, 5, 3, 3, 40, 40, 201, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 386 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113900 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113900 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113900/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113900/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113900 Building REAL300020113901 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113901' /scratch/stefan/7770410/working/building/REAL300020113901 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113901 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113901/0 /scratch/stefan/7770410/working/building/REAL300020113901 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1418) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1418 `/scratch/stefan/7770410/working/3D/1418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN2CCOCC2=N1) `REAL300020113901.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113901 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN2CCOCC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 12, 5, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 20, 20, 20, 20, 1, 1, 13, 54, 87, 87, 87, 87, 87, 87, 87, 87, 54, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 87, 87, 87, 87, 87, 87, 87] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 252 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113901 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN2CCOCC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 12, 5, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [190, 190, 114, 114, 114, 22, 22, 22, 6, 4, 1, 1, 1, 1, 1, 1, 22, 22, 114, 190, 201, 201, 201, 201, 201, 201, 201, 201, 190, 114, 114, 114, 114, 22, 6, 6, 4, 4, 114, 114, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 535 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113901 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN2CCOCC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 12, 5, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 69, 91, 115, 115, 115, 115, 13, 13, 1, 6, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 13, 69, 69, 91, 91, 1, 1, 18, 18, 18, 18, 18, 18, 18] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 424 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113901 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN2CCOCC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 12, 5, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 18, 18, 18, 87, 87, 87, 170, 201, 201, 201, 201, 201, 87, 87, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 18, 18, 18, 18, 87, 170, 170, 201, 201, 18, 18, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 705 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113901 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113901/1 /scratch/stefan/7770410/working/building/REAL300020113901 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1419) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1419 `/scratch/stefan/7770410/working/3D/1419' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN2CCOCC2=N1) `REAL300020113901.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113901/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113901 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN2CCOCC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 12, 5, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 19, 19, 19, 19, 1, 1, 13, 55, 90, 90, 90, 90, 90, 90, 90, 90, 55, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 90, 90, 90, 90, 90, 90, 90] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 257 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113901 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN2CCOCC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 12, 5, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [193, 193, 112, 112, 112, 22, 22, 22, 6, 4, 1, 1, 1, 1, 1, 1, 22, 22, 112, 193, 201, 201, 201, 201, 201, 201, 201, 201, 193, 112, 112, 112, 112, 22, 6, 6, 4, 4, 112, 112, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 544 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113901 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN2CCOCC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 12, 5, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 65, 87, 111, 111, 111, 111, 13, 13, 1, 6, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 13, 65, 65, 87, 87, 1, 1, 18, 18, 18, 18, 18, 18, 18] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 412 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113901 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN2CCOCC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 12, 5, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 18, 18, 18, 90, 90, 90, 170, 201, 201, 201, 201, 201, 90, 90, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 18, 18, 18, 18, 90, 170, 170, 201, 201, 18, 18, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 699 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113901 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113901 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113901/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113901/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113901 Building REAL300020113902 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113902' /scratch/stefan/7770410/working/building/REAL300020113902 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113902 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113902/0 /scratch/stefan/7770410/working/building/REAL300020113902 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1420) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1420 `/scratch/stefan/7770410/working/3D/1420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1) `REAL300020113902.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113902 none NC(=O)C1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 36, 36, 15, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 24, 36, 36, 36, 36, 36, 9, 9, 1, 36, 36, 36, 36, 36, 36, 15, 15, 5, 1, 1, 1, 1, 9, 24, 24, 36, 36, 1, 1, 36] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47]) total number of confs: 234 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113902 none NC(=O)C1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 105, 105, 105, 54, 21, 21, 21, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 9, 105, 105, 105, 105, 105, 105, 54, 54, 21, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 105] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 322 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113902 none NC(=O)C1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 36, 36, 36, 105, 105, 105, 160, 201, 201, 201, 201, 201, 105, 105, 36, 1, 1, 2, 2, 1, 1, 5, 5, 13, 36, 36, 36, 36, 105, 160, 160, 201, 201, 36, 36, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 47, 27, 28, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 747 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113902 none NC(=O)C1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 125, 64, 64, 64, 37, 37, 37, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 37, 201, 201, 201, 201, 201, 201, 125, 125, 64, 37, 37, 37, 37, 8, 4, 4, 2, 2, 37, 37, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 620 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113902 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113902/1 /scratch/stefan/7770410/working/building/REAL300020113902 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1421) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1421 `/scratch/stefan/7770410/working/3D/1421' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1) `REAL300020113902.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113902 none NC(=O)C1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 36, 36, 15, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 24, 36, 36, 36, 36, 36, 9, 9, 1, 36, 36, 36, 36, 36, 36, 15, 15, 5, 1, 1, 1, 1, 9, 24, 24, 36, 36, 1, 1, 36] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47]) total number of confs: 234 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113902 none NC(=O)C1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 105, 105, 105, 54, 21, 21, 21, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 9, 105, 105, 105, 105, 105, 105, 54, 54, 21, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 105] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 322 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113902 none NC(=O)C1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 36, 36, 36, 105, 105, 105, 159, 201, 201, 201, 201, 201, 105, 105, 36, 1, 1, 2, 2, 1, 1, 5, 5, 13, 36, 36, 36, 36, 105, 159, 159, 201, 201, 36, 36, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 47, 27, 28, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 747 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113902 none NC(=O)C1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 126, 64, 64, 64, 37, 37, 37, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 37, 201, 201, 201, 201, 201, 201, 126, 126, 64, 37, 37, 37, 37, 8, 4, 4, 2, 2, 37, 37, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 624 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113902 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113902 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113902/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113902/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113902 Building REAL300020113903 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113903' /scratch/stefan/7770410/working/building/REAL300020113903 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113903 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113903/0 /scratch/stefan/7770410/working/building/REAL300020113903 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1422) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1422 `/scratch/stefan/7770410/working/3D/1422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CS1) `REAL300020113903.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113903 none COCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 31, 25, 25, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 22, 35, 35, 35, 35, 35, 9, 9, 1, 25, 25, 25, 46, 46, 46, 31, 31, 6, 1, 1, 1, 1, 9, 22, 22, 35, 35, 1, 1, 25, 25] 201 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45]) total number of confs: 243 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113903 none COCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [122, 105, 97, 97, 30, 30, 30, 9, 9, 9, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 9, 97, 97, 97, 122, 122, 122, 105, 105, 30, 9, 9, 9, 9, 1, 5, 5, 7, 7, 9, 9, 97, 97] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 265 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113903 none COCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 1, 1, 1, 1, 9, 9, 9, 25, 25, 25, 97, 97, 97, 156, 198, 198, 198, 198, 198, 97, 97, 25, 1, 1, 1, 13, 13, 13, 6, 6, 9, 25, 25, 25, 25, 97, 156, 156, 198, 198, 25, 25, 1, 1] 201 rigid atoms, others: [2, 3, 4, 5, 44, 45, 24, 25, 26] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 762 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113903 none COCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 85, 85, 85, 37, 37, 37, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 37, 201, 201, 201, 201, 201, 201, 201, 201, 85, 37, 37, 37, 37, 8, 4, 4, 2, 2, 37, 37, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 400 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113903 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113903/1 /scratch/stefan/7770410/working/building/REAL300020113903 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1423) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1423 `/scratch/stefan/7770410/working/3D/1423' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CS1) `REAL300020113903.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113903 none COCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 31, 25, 25, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 22, 35, 35, 35, 35, 35, 9, 9, 1, 25, 25, 25, 45, 45, 45, 31, 31, 6, 1, 1, 1, 1, 9, 22, 22, 35, 35, 1, 1, 25, 25] 201 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45]) total number of confs: 241 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113903 none COCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 103, 95, 95, 29, 29, 29, 9, 9, 9, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 9, 95, 95, 95, 120, 120, 120, 103, 103, 29, 9, 9, 9, 9, 1, 5, 5, 7, 7, 9, 9, 95, 95] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 262 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113903 none COCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 1, 1, 1, 1, 9, 9, 9, 25, 25, 25, 95, 95, 95, 155, 198, 198, 198, 198, 198, 95, 95, 25, 1, 1, 1, 13, 13, 13, 6, 6, 9, 25, 25, 25, 25, 95, 155, 155, 198, 198, 25, 25, 1, 1] 201 rigid atoms, others: [2, 3, 4, 5, 44, 45, 24, 25, 26] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 771 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113903 none COCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 85, 85, 85, 37, 37, 37, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 37, 201, 201, 201, 201, 201, 201, 201, 201, 85, 37, 37, 37, 37, 8, 4, 4, 2, 2, 37, 37, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 400 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113903 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113903 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113903/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113903/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113903 Building REAL300020113904 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113904' /scratch/stefan/7770410/working/building/REAL300020113904 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113904 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113904/0 /scratch/stefan/7770410/working/building/REAL300020113904 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1424) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1424 `/scratch/stefan/7770410/working/3D/1424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CCCC1(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113904.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113904 none CCC1CCCC1(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 16, 6, 16, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 37, 53, 53, 53, 53, 53, 13, 13, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 37, 37, 53, 53, 1, 1] 201 rigid atoms, others: [11, 44, 10, 43, 12, 13, 14, 45, 52, 46, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 254 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113904 none CCC1CCCC1(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 107, 107, 46, 107, 46, 46, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 46, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [13, 14, 47, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 343 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113904 none CCC1CCCC1(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 16, 16, 16, 107, 107, 107, 172, 201, 201, 201, 201, 201, 107, 107, 16, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 16, 16, 16, 16, 107, 172, 172, 201, 201, 16, 16] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 8, 7, 34, 35, 36, 38, 37] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 685 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113904 none CCC1CCCC1(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 123, 201, 123, 123, 53, 53, 53, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 53, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 123, 53, 53, 53, 53, 8, 4, 4, 2, 2, 53, 53] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 599 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113904 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113904/1 /scratch/stefan/7770410/working/building/REAL300020113904 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1425) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1425 `/scratch/stefan/7770410/working/3D/1425' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CCCC1(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113904.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113904 none CCC1CCCC1(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 16, 6, 16, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 37, 53, 53, 53, 53, 53, 13, 13, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 37, 37, 53, 53, 1, 1] 201 rigid atoms, others: [11, 44, 10, 43, 12, 13, 14, 45, 52, 46, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 254 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113904 none CCC1CCCC1(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 106, 106, 106, 46, 106, 46, 46, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 46, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [13, 14, 47, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 341 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113904 none CCC1CCCC1(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 16, 16, 16, 106, 106, 106, 172, 201, 201, 201, 201, 201, 106, 106, 16, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 16, 16, 16, 16, 106, 172, 172, 201, 201, 16, 16] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 8, 7, 34, 35, 36, 38, 37] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 681 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113904 none CCC1CCCC1(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 123, 201, 123, 123, 53, 53, 53, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 53, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 123, 53, 53, 53, 53, 8, 4, 4, 2, 2, 53, 53] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 599 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113904 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113904 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113904/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113904/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113904 Building REAL300020113905 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113905' /scratch/stefan/7770410/working/building/REAL300020113905 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113905 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113905/0 /scratch/stefan/7770410/working/building/REAL300020113905 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1426) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1426 `/scratch/stefan/7770410/working/3D/1426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CNC=CC2=N1) `REAL300020113905.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113905 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CNC=CC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 20, 20, 20, 20, 1, 1, 13, 54, 92, 92, 92, 92, 92, 92, 92, 92, 54, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 92, 92, 92, 92, 92] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 263 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113905 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CNC=CC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [187, 187, 115, 115, 115, 22, 22, 22, 6, 4, 1, 1, 1, 1, 1, 1, 22, 22, 115, 187, 201, 201, 201, 201, 201, 201, 201, 201, 187, 115, 115, 115, 115, 22, 6, 6, 4, 4, 115, 115, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 536 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113905 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CNC=CC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 67, 89, 116, 116, 116, 116, 13, 13, 1, 6, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 13, 67, 67, 89, 89, 1, 1, 17, 17, 17, 17, 17] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 423 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113905 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CNC=CC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 17, 17, 17, 92, 92, 92, 170, 201, 201, 201, 201, 201, 92, 92, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 17, 92, 170, 170, 201, 201, 17, 17, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 704 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113905 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113905/1 /scratch/stefan/7770410/working/building/REAL300020113905 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1427) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1427 `/scratch/stefan/7770410/working/3D/1427' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CNC=CC2=N1) `REAL300020113905.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113905/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113905 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CNC=CC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 20, 20, 20, 20, 1, 1, 13, 54, 92, 92, 92, 92, 92, 92, 92, 92, 54, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 92, 92, 92, 92, 92] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 264 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113905 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CNC=CC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [191, 191, 114, 114, 114, 22, 22, 22, 6, 4, 1, 1, 1, 1, 1, 1, 22, 22, 114, 191, 201, 201, 201, 201, 201, 201, 201, 201, 191, 114, 114, 114, 114, 22, 6, 6, 4, 4, 114, 114, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 540 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113905 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CNC=CC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 67, 89, 116, 116, 116, 116, 13, 13, 1, 6, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 13, 67, 67, 89, 89, 1, 1, 18, 18, 18, 18, 18] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 424 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113905 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CNC=CC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 18, 18, 18, 92, 92, 92, 170, 201, 201, 201, 201, 201, 92, 92, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 18, 18, 18, 18, 92, 170, 170, 201, 201, 18, 18, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 702 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113905 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113905 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113905/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113905/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113905 Building REAL300020113906 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113906' /scratch/stefan/7770410/working/building/REAL300020113906 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113906 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113906/0 /scratch/stefan/7770410/working/building/REAL300020113906 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1428) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1428 `/scratch/stefan/7770410/working/3D/1428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C(C)S1) `REAL300020113906.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113906 none CC1=NC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 27, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 31, 45, 49, 49, 49, 49, 9, 9, 1, 32, 32, 32, 32, 32, 32, 27, 27, 6, 1, 1, 1, 1, 9, 31, 31, 45, 45, 1, 1, 32, 32, 32] 201 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 292 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113906 none CC1=NC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 95, 30, 30, 30, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 100, 100, 100, 100, 100, 100, 95, 95, 30, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9, 100, 100, 100] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 388 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113906 none CC1=NC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 4, 13, 13, 13, 32, 32, 32, 100, 100, 100, 167, 201, 201, 201, 201, 201, 100, 100, 32, 1, 1, 1, 2, 2, 2, 4, 4, 13, 32, 32, 32, 32, 100, 167, 167, 201, 201, 32, 32, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 728 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113906 none CC1=NC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 197, 106, 106, 106, 50, 50, 50, 12, 12, 12, 7, 4, 1, 1, 1, 1, 1, 1, 12, 12, 50, 201, 201, 201, 201, 201, 201, 197, 197, 106, 50, 50, 50, 50, 12, 7, 7, 4, 4, 50, 50, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 744 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113906 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113906/1 /scratch/stefan/7770410/working/building/REAL300020113906 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1429) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1429 `/scratch/stefan/7770410/working/3D/1429' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C(C)S1) `REAL300020113906.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113906 none CC1=NC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 27, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 31, 45, 49, 49, 49, 49, 9, 9, 1, 31, 31, 31, 31, 31, 31, 27, 27, 6, 1, 1, 1, 1, 9, 31, 31, 45, 45, 1, 1, 31, 31, 31] 201 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 290 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113906 none CC1=NC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 96, 31, 31, 31, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 100, 100, 100, 100, 100, 100, 96, 96, 31, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9, 100, 100, 100] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 388 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113906 none CC1=NC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 4, 12, 12, 12, 31, 31, 31, 100, 100, 100, 167, 201, 201, 201, 201, 201, 100, 100, 31, 1, 1, 1, 2, 2, 2, 4, 4, 12, 31, 31, 31, 31, 100, 167, 167, 201, 201, 31, 31, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 725 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113906 none CC1=NC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 198, 107, 107, 107, 51, 51, 51, 13, 13, 13, 7, 4, 1, 1, 1, 1, 1, 1, 13, 13, 51, 201, 201, 201, 201, 201, 201, 198, 198, 107, 51, 51, 51, 51, 13, 7, 7, 4, 4, 51, 51, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 745 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113906 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113906 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113906/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113906/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113906 Building REAL300020113907 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113907' /scratch/stefan/7770410/working/building/REAL300020113907 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113907 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113907/0 /scratch/stefan/7770410/working/building/REAL300020113907 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1430) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1430 `/scratch/stefan/7770410/working/3D/1430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CC=C21) `REAL300020113907.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113907 none CN1N=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 30, 45, 50, 50, 50, 50, 9, 9, 1, 16, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 9, 30, 30, 45, 45, 1, 1, 16, 16] 201 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46]) total number of confs: 222 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113907 none CN1N=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 73, 73, 73, 27, 27, 27, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 73, 73, 73, 73, 73, 73, 73, 27, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9, 73, 73] 201 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 174 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113907 none CN1N=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 73, 73, 73, 143, 201, 201, 201, 201, 201, 73, 73, 16, 1, 1, 1, 2, 2, 2, 1, 5, 16, 16, 16, 16, 73, 143, 143, 201, 201, 16, 16, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 45, 46, 26, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 829 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113907 none CN1N=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 80, 80, 80, 51, 51, 51, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 51, 201, 201, 201, 201, 201, 201, 201, 80, 51, 51, 51, 51, 12, 6, 6, 4, 4, 51, 51, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 408 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113907 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113907/1 /scratch/stefan/7770410/working/building/REAL300020113907 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1431) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1431 `/scratch/stefan/7770410/working/3D/1431' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CC=C21) `REAL300020113907.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113907 none CN1N=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 30, 45, 50, 50, 50, 50, 9, 9, 1, 16, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 9, 30, 30, 45, 45, 1, 1, 16, 16] 201 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46]) total number of confs: 222 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113907 none CN1N=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 74, 74, 74, 27, 27, 27, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 74, 74, 74, 74, 74, 74, 74, 27, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9, 74, 74] 201 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 175 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113907 none CN1N=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 74, 74, 74, 143, 201, 201, 201, 201, 201, 74, 74, 16, 1, 1, 1, 2, 2, 2, 1, 5, 16, 16, 16, 16, 74, 143, 143, 201, 201, 16, 16, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 45, 46, 26, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 827 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113907 none CN1N=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 80, 80, 80, 50, 50, 50, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 50, 201, 201, 201, 201, 201, 201, 201, 80, 50, 50, 50, 50, 11, 6, 6, 4, 4, 50, 50, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 409 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113907 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113907 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113907/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113907/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113907 Building REAL300020113908 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113908' /scratch/stefan/7770410/working/building/REAL300020113908 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113908 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113908/0 /scratch/stefan/7770410/working/building/REAL300020113908 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1432) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1432 `/scratch/stefan/7770410/working/3D/1432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(C)(C)C) `REAL300020113908.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113908 none CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 48, 48, 48, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 17, 17, 17, 17, 1, 1, 12, 82, 82, 82, 82, 82, 82, 82, 82, 48, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 82, 82, 82, 82, 82, 82, 82, 82, 82] 201 rigid atoms, others: [34, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 366 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113908 none CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 155, 155, 155, 85, 85, 85, 20, 20, 20, 6, 4, 1, 1, 1, 1, 1, 1, 20, 20, 85, 201, 201, 201, 201, 201, 201, 201, 201, 155, 85, 85, 85, 85, 20, 6, 6, 4, 4, 85, 85, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 696 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113908 none CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 54, 72, 85, 85, 85, 85, 12, 12, 1, 13, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 12, 54, 54, 72, 72, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 39, 40, 20, 30, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 351 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113908 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113908/1 /scratch/stefan/7770410/working/building/REAL300020113908 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1433) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1433 `/scratch/stefan/7770410/working/3D/1433' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(C)(C)C) `REAL300020113908.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113908/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113908 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 48, 48, 48, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 17, 17, 17, 17, 1, 1, 12, 82, 82, 82, 82, 82, 82, 82, 82, 48, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 82, 82, 82, 82, 82, 82, 82, 82, 82] 201 rigid atoms, others: [34, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 366 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113908 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 154, 154, 154, 84, 84, 84, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 84, 201, 201, 201, 201, 201, 201, 201, 201, 154, 84, 84, 84, 84, 18, 6, 6, 4, 4, 84, 84, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 702 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113908 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 52, 70, 84, 84, 84, 84, 12, 12, 1, 13, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 12, 52, 52, 70, 70, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 39, 40, 20, 30, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 347 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113908 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113908 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113908/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113908/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113908 Building REAL300020113909 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113909' /scratch/stefan/7770410/working/building/REAL300020113909 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113909 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113909/0 /scratch/stefan/7770410/working/building/REAL300020113909 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1434) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1434 `/scratch/stefan/7770410/working/3D/1434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC2=CC=CC=C21) `REAL300020113909.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113909 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 59, 99, 99, 99, 99, 99, 99, 99, 99, 99, 59, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 323 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113909 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 55, 55, 55, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 55, 162, 201, 201, 201, 201, 201, 201, 201, 201, 201, 162, 55, 55, 55, 55, 10, 6, 6, 4, 4, 55, 55, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 581 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113909 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 32, 50, 55, 55, 55, 55, 13, 13, 1, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 32, 32, 50, 50, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 261 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113909 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 16, 16, 16, 99, 99, 99, 157, 201, 201, 201, 201, 201, 99, 99, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 16, 99, 157, 157, 201, 201, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 698 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113909 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113909/1 /scratch/stefan/7770410/working/building/REAL300020113909 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1435) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1435 `/scratch/stefan/7770410/working/3D/1435' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2=CC=CC=C21) `REAL300020113909.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113909 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 59, 99, 99, 99, 99, 99, 99, 99, 99, 99, 59, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 323 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113909 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 55, 55, 55, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 55, 162, 201, 201, 201, 201, 201, 201, 201, 201, 201, 162, 55, 55, 55, 55, 10, 6, 6, 4, 4, 55, 55, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 581 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113909 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 32, 50, 55, 55, 55, 55, 13, 13, 1, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 32, 32, 50, 50, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 261 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113909 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 16, 16, 16, 99, 99, 99, 157, 201, 201, 201, 201, 201, 99, 99, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 16, 99, 157, 157, 201, 201, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 698 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113909 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113909 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113909/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113909/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113909 Building REAL300020113910 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113910' /scratch/stefan/7770410/working/building/REAL300020113910 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113910 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113910/0 /scratch/stefan/7770410/working/building/REAL300020113910 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1436) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1436 `/scratch/stefan/7770410/working/3D/1436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=C(F)C=C1) `REAL300020113910.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113910 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 56, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 56, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 156, 156, 156, 156, 156, 156] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 461 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113910 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 3, 20, 20, 51, 51, 51, 156, 156, 156, 184, 201, 201, 201, 201, 201, 156, 156, 51, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 20, 51, 51, 51, 51, 156, 184, 184, 201, 201, 51, 51, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [45, 46, 47, 48, 22, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 525 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113910 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 43, 43, 43, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 43, 103, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 103, 43, 43, 43, 43, 8, 4, 4, 2, 2, 43, 43, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 595 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113910 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 27, 36, 36, 36, 36, 36, 13, 13, 1, 6, 41, 41, 41, 41, 41, 51, 51, 41, 41, 51, 51, 6, 1, 1, 1, 1, 13, 27, 27, 36, 36, 1, 1, 41, 41, 51, 51, 51, 51] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 41, 42, 34, 18, 35] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48]) total number of confs: 279 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113910 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 41, 41, 41, 156, 156, 156, 184, 201, 201, 201, 201, 201, 156, 156, 41, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 41, 41, 41, 41, 156, 184, 184, 201, 201, 41, 41, 1, 1, 3, 3, 3, 3] 201 rigid atoms, others: [1, 43, 44, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48]) total number of confs: 510 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113910 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113910/1 /scratch/stefan/7770410/working/building/REAL300020113910 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1437) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1437 `/scratch/stefan/7770410/working/3D/1437' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=C(F)C=C1) `REAL300020113910.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113910 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 56, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 56, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 156, 156, 156, 156, 156, 156] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 461 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113910 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 3, 20, 20, 51, 51, 51, 156, 156, 156, 184, 201, 201, 201, 201, 201, 156, 156, 51, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 20, 51, 51, 51, 51, 156, 184, 184, 201, 201, 51, 51, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [45, 46, 47, 48, 22, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 525 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113910 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 43, 43, 43, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 43, 103, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 103, 43, 43, 43, 43, 8, 4, 4, 2, 2, 43, 43, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 595 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113910 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 27, 36, 36, 36, 36, 36, 13, 13, 1, 6, 41, 41, 41, 41, 41, 51, 51, 41, 41, 51, 51, 6, 1, 1, 1, 1, 13, 27, 27, 36, 36, 1, 1, 41, 41, 51, 51, 51, 51] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 41, 42, 34, 18, 35] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48]) total number of confs: 279 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113910 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[C@@H]1C[C@H]1C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 41, 41, 41, 156, 156, 156, 184, 201, 201, 201, 201, 201, 156, 156, 41, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 41, 41, 41, 41, 156, 184, 184, 201, 201, 41, 41, 1, 1, 3, 3, 3, 3] 201 rigid atoms, others: [1, 43, 44, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48]) total number of confs: 510 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113910 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113910 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113910/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113910/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113910 Building REAL300020113911 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113911' /scratch/stefan/7770410/working/building/REAL300020113911 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113911 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113911/0 /scratch/stefan/7770410/working/building/REAL300020113911 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1438) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1438 `/scratch/stefan/7770410/working/3D/1438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCC1) `REAL300020113911.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113911 none COCCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 14, 12, 11, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 38, 55, 57, 57, 57, 57, 13, 13, 1, 11, 11, 11, 11, 29, 29, 29, 14, 14, 12, 12, 6, 1, 1, 1, 1, 13, 38, 38, 55, 55, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 45, 46, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 299 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113911 none COCCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 77, 74, 74, 59, 59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 74, 74, 74, 74, 107, 107, 107, 77, 77, 74, 74, 59, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 74, 74, 74, 74, 74, 74, 74, 74] 201 rigid atoms, others: [40, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 311 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113911 none COCCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 4, 1, 1, 1, 3, 3, 3, 11, 11, 11, 74, 74, 74, 143, 199, 199, 199, 199, 199, 74, 74, 11, 1, 1, 1, 1, 10, 10, 10, 5, 5, 4, 4, 3, 11, 11, 11, 11, 74, 143, 143, 199, 199, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 47, 48, 49, 50, 51, 52, 53, 54, 24, 25, 26, 27] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 800 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113911 none COCCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 188, 188, 188, 59, 59, 59, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 59, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 188, 59, 59, 59, 59, 10, 6, 6, 4, 4, 59, 59, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 547 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113911 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113911/1 /scratch/stefan/7770410/working/building/REAL300020113911 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1439) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1439 `/scratch/stefan/7770410/working/3D/1439' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCC1) `REAL300020113911.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113911 none COCCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 14, 12, 11, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 38, 55, 57, 57, 57, 57, 13, 13, 1, 11, 11, 11, 11, 28, 28, 28, 14, 14, 12, 12, 6, 1, 1, 1, 1, 13, 38, 38, 55, 55, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 45, 46, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 298 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113911 none COCCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 78, 75, 75, 59, 59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 75, 75, 75, 75, 106, 106, 106, 78, 78, 75, 75, 59, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 75, 75, 75, 75, 75, 75, 75, 75] 201 rigid atoms, others: [40, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 312 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113911 none COCCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 4, 1, 1, 1, 3, 3, 3, 11, 11, 11, 75, 75, 75, 144, 199, 199, 199, 199, 199, 75, 75, 11, 1, 1, 1, 1, 10, 10, 10, 5, 5, 4, 4, 3, 11, 11, 11, 11, 75, 144, 144, 199, 199, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 47, 48, 49, 50, 51, 52, 53, 54, 24, 25, 26, 27] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 795 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113911 none COCCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 188, 188, 188, 59, 59, 59, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 59, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 188, 59, 59, 59, 59, 10, 6, 6, 4, 4, 59, 59, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 545 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113911 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113911 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113911/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113911/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113911 Building REAL300020113912 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113912' /scratch/stefan/7770410/working/building/REAL300020113912 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113912 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113912/0 /scratch/stefan/7770410/working/building/REAL300020113912 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1440) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1440 `/scratch/stefan/7770410/working/3D/1440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1CCCO1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113912.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113912 none CC(CC1CCCO1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 17, 23, 33, 33, 33, 33, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 35, 48, 55, 55, 55, 55, 9, 9, 1, 17, 17, 17, 17, 23, 23, 33, 33, 33, 33, 33, 33, 33, 6, 1, 1, 1, 1, 9, 35, 35, 48, 48, 1, 1] 201 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 44, 50, 51, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 337 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113912 none CC(CC1CCCO1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 25, 70, 92, 112, 112, 112, 112, 25, 25, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 70, 70, 70, 70, 92, 92, 112, 112, 112, 112, 112, 112, 112, 25, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9] 201 rigid atoms, others: [45, 14, 13, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 500 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113912 none CC(CC1CCCO1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 5, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 33, 33, 33, 112, 112, 112, 178, 201, 201, 201, 201, 201, 112, 112, 33, 6, 6, 6, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 15, 33, 33, 33, 33, 112, 178, 178, 201, 201, 33, 33] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 39, 34, 35, 36, 38, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 694 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113912 none CC(CC1CCCO1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 103, 199, 199, 201, 201, 201, 201, 103, 103, 58, 58, 58, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 58, 199, 199, 199, 199, 199, 199, 201, 201, 201, 201, 201, 201, 201, 103, 58, 58, 58, 58, 13, 6, 6, 4, 4, 58, 58] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 754 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113912 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113912/1 /scratch/stefan/7770410/working/building/REAL300020113912 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1441) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1441 `/scratch/stefan/7770410/working/3D/1441' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1CCCO1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113912.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113912 none CC(CC1CCCO1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 17, 23, 33, 33, 33, 33, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 35, 48, 55, 55, 55, 55, 9, 9, 1, 17, 17, 17, 17, 23, 23, 33, 33, 33, 33, 33, 33, 33, 6, 1, 1, 1, 1, 9, 35, 35, 48, 48, 1, 1] 201 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 44, 50, 51, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 337 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113912 none CC(CC1CCCO1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 25, 70, 92, 112, 112, 112, 112, 25, 25, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 70, 70, 70, 70, 92, 92, 112, 112, 112, 112, 112, 112, 112, 25, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9] 201 rigid atoms, others: [45, 14, 13, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 500 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113912 none CC(CC1CCCO1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 5, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 33, 33, 33, 112, 112, 112, 178, 201, 201, 201, 201, 201, 112, 112, 33, 6, 6, 6, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 15, 33, 33, 33, 33, 112, 178, 178, 201, 201, 33, 33] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 39, 34, 35, 36, 38, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 694 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113912 none CC(CC1CCCO1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 104, 199, 199, 201, 201, 201, 201, 104, 104, 58, 58, 58, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 58, 199, 199, 199, 199, 199, 199, 201, 201, 201, 201, 201, 201, 201, 104, 58, 58, 58, 58, 12, 6, 6, 4, 4, 58, 58] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 756 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113912 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113912 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113912/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113912/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113912 Building REAL300020113913 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113913' /scratch/stefan/7770410/working/building/REAL300020113913 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113913 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113913/0 /scratch/stefan/7770410/working/building/REAL300020113913 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1442) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1442 `/scratch/stefan/7770410/working/3D/1442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CO1) `REAL300020113913.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113913 none CC(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 32, 48, 56, 56, 56, 56, 11, 11, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 32, 32, 48, 48, 1, 1, 22, 22] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 44, 45, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47]) total number of confs: 244 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113913 none CC(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 102, 32, 32, 32, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 32, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 102, 102] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 210 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113913 none CC(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 22, 22, 22, 102, 102, 102, 153, 201, 201, 201, 201, 201, 102, 102, 22, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 7, 22, 22, 22, 22, 102, 153, 153, 201, 201, 22, 22, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 46, 47, 24, 25, 26, 5, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 724 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113913 none CC(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 103, 103, 103, 56, 56, 56, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 56, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 103, 56, 56, 56, 56, 10, 6, 6, 4, 4, 56, 56, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 460 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113913 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113913/1 /scratch/stefan/7770410/working/building/REAL300020113913 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1443) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1443 `/scratch/stefan/7770410/working/3D/1443' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CO1) `REAL300020113913.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113913 none CC(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 32, 47, 55, 55, 55, 55, 11, 11, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 32, 32, 47, 47, 1, 1, 22, 22] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 44, 45, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47]) total number of confs: 238 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113913 none CC(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 102, 32, 32, 32, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 32, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 102, 102] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 210 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113913 none CC(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 22, 22, 22, 102, 102, 102, 154, 201, 201, 201, 201, 201, 102, 102, 22, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 7, 22, 22, 22, 22, 102, 154, 154, 201, 201, 22, 22, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 46, 47, 24, 25, 26, 5, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 724 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113913 none CC(C)C1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 102, 102, 102, 55, 55, 55, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 55, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 102, 55, 55, 55, 55, 10, 6, 6, 4, 4, 55, 55, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 459 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113913 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113913 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113913/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113913/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113913 Building REAL300020113914 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113914' /scratch/stefan/7770410/working/building/REAL300020113914 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113914 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113914/0 /scratch/stefan/7770410/working/building/REAL300020113914 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1444) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1444 `/scratch/stefan/7770410/working/3D/1444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCCCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113914.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113914 none CCOCCCCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 124, 58, 71, 58, 54, 14, 14, 14, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 125, 125, 125, 125, 125, 115, 117, 71, 71, 71, 71, 71, 71, 54, 54, 14, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [13, 14, 47, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 717 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113914 none CCOCCCCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 123, 147, 123, 124, 25, 25, 25, 25, 25, 25, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 25, 201, 201, 201, 201, 201, 189, 189, 147, 147, 147, 147, 147, 147, 124, 124, 25, 25, 25, 25, 25, 7, 4, 4, 2, 2, 25, 25] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 1105 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113914 none CCOCCCCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 62, 24, 31, 24, 20, 4, 4, 4, 1, 1, 1, 1, 1, 7, 7, 7, 15, 24, 24, 24, 24, 24, 7, 7, 1, 63, 63, 63, 63, 63, 56, 57, 31, 31, 31, 31, 31, 31, 20, 20, 4, 1, 1, 1, 1, 7, 15, 15, 24, 24, 1, 1] 201 rigid atoms, others: [11, 44, 10, 43, 12, 13, 14, 45, 52, 46, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 440 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113914 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113914/1 /scratch/stefan/7770410/working/building/REAL300020113914 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1445) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1445 `/scratch/stefan/7770410/working/3D/1445' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCCCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113914.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113914/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113914 none CCOCCCCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 124, 58, 71, 58, 54, 14, 14, 14, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 125, 125, 125, 125, 125, 115, 117, 71, 71, 71, 71, 71, 71, 54, 54, 14, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [13, 14, 47, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 717 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113914 none CCOCCCCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 123, 147, 123, 124, 25, 25, 25, 25, 25, 25, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 25, 201, 201, 201, 201, 201, 189, 189, 147, 147, 147, 147, 147, 147, 124, 124, 25, 25, 25, 25, 25, 7, 4, 4, 2, 2, 25, 25] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 1107 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113914 none CCOCCCCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 62, 24, 31, 24, 20, 4, 4, 4, 1, 1, 1, 1, 1, 7, 7, 7, 15, 24, 24, 24, 24, 24, 7, 7, 1, 63, 63, 63, 63, 63, 56, 57, 31, 31, 31, 31, 31, 31, 20, 20, 4, 1, 1, 1, 1, 7, 15, 15, 24, 24, 1, 1] 201 rigid atoms, others: [11, 44, 10, 43, 12, 13, 14, 45, 52, 46, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 440 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113914 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113914 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113914/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113914/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113914 Building REAL300020113915 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113915' /scratch/stefan/7770410/working/building/REAL300020113915 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113915 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113915/0 /scratch/stefan/7770410/working/building/REAL300020113915 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1446) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1446 `/scratch/stefan/7770410/working/3D/1446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113915.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113915 none CNC(=O)CCCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [141, 141, 106, 141, 93, 80, 73, 18, 18, 18, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 141, 141, 141, 141, 106, 106, 93, 93, 93, 93, 73, 73, 18, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [44, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 679 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113915 none CNC(=O)CCCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 187, 201, 162, 140, 127, 40, 40, 40, 31, 31, 31, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 31, 201, 201, 201, 201, 187, 187, 162, 162, 162, 162, 127, 127, 40, 31, 31, 31, 31, 8, 4, 4, 2, 2, 31, 31] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 989 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113915 none CNC(=O)CCCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 47, 64, 35, 27, 23, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 19, 29, 29, 29, 29, 29, 7, 7, 1, 64, 64, 64, 64, 47, 47, 35, 35, 35, 35, 23, 23, 5, 1, 1, 1, 1, 7, 19, 19, 29, 29, 1, 1] 201 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 49, 50, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 450 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113915 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113915/1 /scratch/stefan/7770410/working/building/REAL300020113915 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1447) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1447 `/scratch/stefan/7770410/working/3D/1447' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113915.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113915 none CNC(=O)CCCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [143, 143, 107, 143, 93, 80, 73, 18, 18, 18, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 143, 143, 143, 143, 107, 107, 93, 93, 93, 93, 73, 73, 18, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [44, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 689 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113915 none CNC(=O)CCCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 186, 201, 162, 139, 127, 40, 40, 40, 31, 31, 31, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 31, 201, 201, 201, 201, 186, 186, 162, 162, 162, 162, 127, 127, 40, 31, 31, 31, 31, 8, 4, 4, 2, 2, 31, 31] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 994 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113915 none CNC(=O)CCCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 48, 66, 35, 27, 23, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 19, 29, 29, 29, 29, 29, 7, 7, 1, 66, 66, 66, 66, 48, 48, 35, 35, 35, 35, 23, 23, 5, 1, 1, 1, 1, 7, 19, 19, 29, 29, 1, 1] 201 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 49, 50, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 458 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113915 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113915 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113915/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113915/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113915 Building REAL300020113916 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113916' /scratch/stefan/7770410/working/building/REAL300020113916 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113916 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113916/0 /scratch/stefan/7770410/working/building/REAL300020113916 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1448) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1448 `/scratch/stefan/7770410/working/3D/1448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CS(C)(=O)=O)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113916.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113916 none CC(C)(CS(C)(=O)=O)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 5, 11, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 25, 84, 84, 108, 108, 108, 108, 25, 25, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 84, 84, 84, 84, 84, 84, 108, 108, 108, 108, 108, 25, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 475 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113916 none CC(C)(CS(C)(=O)=O)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 5, 11, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [170, 113, 170, 170, 201, 201, 201, 201, 113, 113, 58, 58, 58, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 58, 170, 170, 170, 170, 170, 170, 201, 201, 201, 201, 201, 113, 58, 58, 58, 58, 14, 6, 6, 4, 4, 58, 58] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 789 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113916 none CC(C)(CS(C)(=O)=O)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 5, 11, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 5, 20, 20, 27, 27, 27, 27, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 26, 40, 41, 41, 41, 41, 8, 8, 1, 20, 20, 20, 20, 20, 20, 27, 27, 27, 27, 27, 5, 1, 1, 1, 1, 8, 26, 26, 40, 40, 1, 1] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113916 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113916/1 /scratch/stefan/7770410/working/building/REAL300020113916 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1449) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1449 `/scratch/stefan/7770410/working/3D/1449' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CS(C)(=O)=O)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113916.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113916 none CC(C)(CS(C)(=O)=O)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 5, 11, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 25, 84, 84, 108, 108, 108, 108, 25, 25, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 84, 84, 84, 84, 84, 84, 108, 108, 108, 108, 108, 25, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 475 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113916 none CC(C)(CS(C)(=O)=O)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 5, 11, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [170, 113, 170, 170, 201, 201, 201, 201, 113, 113, 58, 58, 58, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 58, 170, 170, 170, 170, 170, 170, 201, 201, 201, 201, 201, 113, 58, 58, 58, 58, 14, 6, 6, 4, 4, 58, 58] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 789 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113916 none CC(C)(CS(C)(=O)=O)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 5, 11, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 5, 20, 20, 27, 27, 27, 27, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 25, 39, 40, 40, 40, 40, 8, 8, 1, 20, 20, 20, 20, 20, 20, 27, 27, 27, 27, 27, 5, 1, 1, 1, 1, 8, 25, 25, 39, 39, 1, 1] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 276 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113916 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113916 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113916/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113916/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113916 Building REAL300020113917 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113917' /scratch/stefan/7770410/working/building/REAL300020113917 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113917 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113917/0 /scratch/stefan/7770410/working/building/REAL300020113917 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1450) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1450 `/scratch/stefan/7770410/working/3D/1450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCC2=CC=CC=C21) `REAL300020113917.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113917 none CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 38, 55, 66, 66, 66, 66, 11, 11, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 11, 38, 38, 55, 55, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 42, 43, 20, 36] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 295 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113917 none CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 42, 42, 42, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 85, 85, 85, 85, 85, 85, 85, 85, 85, 85, 85, 42, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 85, 85, 85, 85, 85, 85, 85, 85] 201 rigid atoms, others: [37, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 281 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113917 none CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 8, 8, 8, 19, 19, 19, 85, 85, 85, 161, 201, 201, 201, 201, 201, 85, 85, 19, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 19, 19, 19, 19, 85, 161, 161, 201, 201, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 44, 45, 46, 47, 48, 49, 50, 51, 21, 22, 23, 24, 25, 26, 27, 28] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 743 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113917 none CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 129, 129, 129, 66, 66, 66, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 66, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 129, 66, 66, 66, 66, 13, 6, 6, 4, 4, 66, 66, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 589 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113917 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113917/1 /scratch/stefan/7770410/working/building/REAL300020113917 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1451) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1451 `/scratch/stefan/7770410/working/3D/1451' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC2=CC=CC=C21) `REAL300020113917.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113917/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113917 none CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 40, 57, 67, 67, 67, 67, 11, 11, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 11, 40, 40, 57, 57, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 42, 43, 20, 36] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 299 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113917 none CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 42, 42, 42, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 42, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 86, 86, 86, 86, 86, 86, 86, 86] 201 rigid atoms, others: [37, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 285 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113917 none CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 8, 8, 8, 19, 19, 19, 86, 86, 86, 163, 201, 201, 201, 201, 201, 86, 86, 19, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 19, 19, 19, 19, 86, 163, 163, 201, 201, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 44, 45, 46, 47, 48, 49, 50, 51, 21, 22, 23, 24, 25, 26, 27, 28] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 741 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113917 none CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 130, 130, 130, 68, 68, 68, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 68, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 130, 68, 68, 68, 68, 14, 6, 6, 4, 4, 68, 68, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 584 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113917 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113917 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113917/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113917/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113917 Building REAL300020113918 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113918' /scratch/stefan/7770410/working/building/REAL300020113918 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113918 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113918/0 /scratch/stefan/7770410/working/building/REAL300020113918 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1452) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1452 `/scratch/stefan/7770410/working/3D/1452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1) `REAL300020113918.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113918 none CC(C)(C)C1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 25, 25, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 34, 48, 52, 52, 52, 52, 11, 11, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 1, 1, 1, 1, 11, 34, 34, 48, 48, 1, 1, 25, 25] 201 rigid atoms, others: [43, 9, 10, 11, 12, 13, 44, 50, 51, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 252 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113918 none CC(C)(C)C1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 99, 99, 99, 25, 25, 25, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 25, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 99, 99] 201 rigid atoms, others: [12, 45, 14, 13, 16, 23, 24, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 285 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113918 none CC(C)(C)C1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 11, 11, 11, 25, 25, 25, 99, 99, 99, 161, 201, 201, 201, 201, 201, 99, 99, 25, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 11, 25, 25, 25, 25, 99, 161, 161, 201, 201, 25, 25, 1, 1] 201 rigid atoms, others: [1, 4, 5, 6, 7, 39, 52, 53, 36, 26, 38, 37] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 719 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113918 none CC(C)(C)C1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 90, 90, 90, 52, 52, 52, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 52, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 90, 52, 52, 52, 52, 11, 6, 6, 4, 4, 52, 52, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 603 number of broken/clashed sets: 201 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113918 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113918/1 /scratch/stefan/7770410/working/building/REAL300020113918 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1453) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1453 `/scratch/stefan/7770410/working/3D/1453' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1) `REAL300020113918.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113918 none CC(C)(C)C1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 25, 25, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 47, 51, 51, 51, 51, 11, 11, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 1, 1, 1, 1, 11, 33, 33, 47, 47, 1, 1, 25, 25] 201 rigid atoms, others: [43, 9, 10, 11, 12, 13, 44, 50, 51, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 249 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113918 none CC(C)(C)C1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 98, 98, 98, 25, 25, 25, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 25, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 98, 98] 201 rigid atoms, others: [12, 45, 14, 13, 16, 23, 24, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 283 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113918 none CC(C)(C)C1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 11, 11, 11, 25, 25, 25, 98, 98, 98, 161, 201, 201, 201, 201, 201, 98, 98, 25, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 11, 25, 25, 25, 25, 98, 161, 161, 201, 201, 25, 25, 1, 1] 201 rigid atoms, others: [1, 4, 5, 6, 7, 39, 52, 53, 36, 26, 38, 37] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 721 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113918 none CC(C)(C)C1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 89, 89, 89, 51, 51, 51, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 51, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 89, 51, 51, 51, 51, 10, 6, 6, 4, 4, 51, 51, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 605 number of broken/clashed sets: 201 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113918 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113918 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113918/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113918/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113918 Building REAL300020113919 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113919' /scratch/stefan/7770410/working/building/REAL300020113919 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113919 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113919/0 /scratch/stefan/7770410/working/building/REAL300020113919 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1454) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1454 `/scratch/stefan/7770410/working/3D/1454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1C) `REAL300020113919.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113919 none CC1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 45, 48, 48, 48, 48, 11, 11, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 11, 31, 31, 45, 45, 1, 1, 15, 15, 15, 15, 15, 15] 201 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 46, 47, 40, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50, 51, 52, 53]) total number of confs: 229 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113919 none CC1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 76, 41, 41, 41, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 41, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 76, 76, 76, 76, 76, 76] 201 rigid atoms, others: [41, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 257 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113919 none CC1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 15, 15, 15, 76, 76, 76, 157, 201, 201, 201, 201, 201, 76, 76, 15, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 15, 15, 15, 15, 76, 157, 157, 201, 201, 15, 15, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 51, 32, 34, 48, 49, 50, 35, 52, 53, 24, 25, 26, 5, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 758 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113919 none CC1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 129, 129, 129, 48, 48, 48, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 48, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 129, 48, 48, 48, 48, 10, 6, 6, 4, 4, 48, 48, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 609 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113919 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113919/1 /scratch/stefan/7770410/working/building/REAL300020113919 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1455) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1455 `/scratch/stefan/7770410/working/3D/1455' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1C) `REAL300020113919.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113919/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113919 none CC1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 45, 48, 48, 48, 48, 11, 11, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 11, 31, 31, 45, 45, 1, 1, 15, 15, 15, 15, 15, 15] 201 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 46, 47, 40, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50, 51, 52, 53]) total number of confs: 229 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113919 none CC1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 76, 41, 41, 41, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 41, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 76, 76, 76, 76, 76, 76] 201 rigid atoms, others: [41, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 257 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113919 none CC1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 15, 15, 15, 76, 76, 76, 157, 201, 201, 201, 201, 201, 76, 76, 15, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 15, 15, 15, 15, 76, 157, 157, 201, 201, 15, 15, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 51, 32, 34, 48, 49, 50, 35, 52, 53, 24, 25, 26, 5, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 758 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113919 none CC1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 129, 129, 129, 48, 48, 48, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 48, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 129, 48, 48, 48, 48, 10, 6, 6, 4, 4, 48, 48, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 609 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113919 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113919 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113919/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113919/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113919 Building REAL300020113920 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113920' /scratch/stefan/7770410/working/building/REAL300020113920 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113920 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113920/0 /scratch/stefan/7770410/working/building/REAL300020113920 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1456) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1456 `/scratch/stefan/7770410/working/3D/1456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CCCCC1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113920.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113920 none COC1CCCCC1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 45, 62, 77, 77, 77, 77, 12, 12, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 12, 45, 45, 62, 62, 1, 1] 201 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 44, 50, 51, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 325 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113920 none COC1CCCCC1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 100, 100, 100, 100, 45, 45, 45, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 12, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 45, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12] 201 rigid atoms, others: [45, 14, 13, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 308 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113920 none COC1CCCCC1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 22, 22, 22, 100, 100, 100, 170, 201, 201, 201, 201, 201, 100, 100, 22, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 22, 22, 22, 22, 100, 170, 170, 201, 201, 22, 22] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 39, 34, 35, 36, 33, 38, 37, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 702 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113920 none COC1CCCCC1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 133, 133, 133, 68, 68, 68, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 68, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 133, 68, 68, 68, 68, 14, 6, 6, 4, 4, 68, 68] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 629 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113920 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113920/1 /scratch/stefan/7770410/working/building/REAL300020113920 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1457) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1457 `/scratch/stefan/7770410/working/3D/1457' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113920.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113920 none COC1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 44, 61, 76, 76, 76, 76, 12, 12, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 12, 44, 44, 61, 61, 1, 1] 201 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 44, 50, 51, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 322 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113920 none COC1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 99, 99, 99, 99, 45, 45, 45, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 12, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 45, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12] 201 rigid atoms, others: [45, 14, 13, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 306 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113920 none COC1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 22, 22, 22, 99, 99, 99, 170, 201, 201, 201, 201, 201, 99, 99, 22, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 22, 22, 22, 22, 99, 170, 170, 201, 201, 22, 22] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 39, 34, 35, 36, 33, 38, 37, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 707 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113920 none COC1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 132, 132, 132, 69, 69, 69, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 69, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 132, 69, 69, 69, 69, 15, 6, 6, 4, 4, 69, 69] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 628 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113920 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113920 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113920/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113920/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113920 Building REAL300020113921 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113921' /scratch/stefan/7770410/working/building/REAL300020113921 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300020113921 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113921/0 /scratch/stefan/7770410/working/building/REAL300020113921 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1458) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1458 `/scratch/stefan/7770410/working/3D/1458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[NH+]1C(C)CCC1C) `REAL300020113921.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113921 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[NH+]1C(C)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 9, 6, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [28, 27, 27, 27, 12, 12, 12, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 27, 12, 12, 12, 12, 1, 4, 4, 4, 4, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 29 rigid atoms, others: [38, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 91 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113921 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[NH+]1C(C)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 9, 6, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 28, 28, 28, 13, 13, 13, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 28, 13, 13, 13, 13, 4, 3, 3, 1, 1, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 29 rigid atoms, others: [41, 42, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 88 number of broken/clashed sets: 29 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113921 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[NH+]1C(C)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 9, 6, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 1, 12, 12, 12, 13, 13, 13, 13, 13, 13, 12, 12, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 12, 13, 13, 13, 13, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 29 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 43, 44, 20, 36, 37] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 50 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113921 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)[NH+]1C(C)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 9, 6, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 4, 4, 9, 9, 9, 28, 28, 28, 29, 29, 29, 29, 29, 29, 28, 28, 9, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 9, 9, 9, 9, 28, 29, 29, 29, 29, 9, 9, 1, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2] 29 rigid atoms, others: [1, 45, 49, 50, 51, 52, 21, 22, 23, 24, 25, 26, 27, 28, 53] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 54, 55, 56]) total number of confs: 70 number of broken/clashed sets: 29 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113921 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113921 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 0: /scratch/stefan/7770410/working/building/REAL300020113921/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113921 Building REAL300020113922 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113922' /scratch/stefan/7770410/working/building/REAL300020113922 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113922 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113922/0 /scratch/stefan/7770410/working/building/REAL300020113922 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1459) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1459 `/scratch/stefan/7770410/working/3D/1459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCOCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113922.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113922 none C=CCCOCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 113, 63, 50, 40, 15, 15, 15, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 117, 117, 117, 113, 113, 63, 63, 40, 40, 15, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [39, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 524 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113922 none C=CCCOCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 106, 87, 78, 33, 33, 33, 26, 26, 26, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 26, 201, 201, 201, 201, 201, 106, 106, 78, 78, 33, 26, 26, 26, 26, 7, 4, 4, 2, 2, 26, 26] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 889 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113922 none C=CCCOCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 44, 26, 19, 11, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 19, 30, 30, 30, 30, 30, 7, 7, 1, 50, 50, 50, 44, 44, 26, 26, 11, 11, 5, 1, 1, 1, 1, 7, 19, 19, 30, 30, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 11, 12, 45, 44, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 322 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113922 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113922/1 /scratch/stefan/7770410/working/building/REAL300020113922 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1460) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1460 `/scratch/stefan/7770410/working/3D/1460' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCOCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113922.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113922/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113922 none C=CCCOCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 113, 63, 50, 40, 15, 15, 15, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 117, 117, 117, 113, 113, 63, 63, 40, 40, 15, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [39, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 524 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113922 none C=CCCOCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 106, 87, 78, 32, 32, 32, 26, 26, 26, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 26, 201, 201, 201, 201, 201, 106, 106, 78, 78, 32, 26, 26, 26, 26, 7, 4, 4, 2, 2, 26, 26] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 893 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113922 none C=CCCOCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 44, 26, 19, 11, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 19, 30, 30, 30, 30, 30, 7, 7, 1, 50, 50, 50, 44, 44, 26, 26, 11, 11, 5, 1, 1, 1, 1, 7, 19, 19, 30, 30, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 11, 12, 45, 44, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 322 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113922 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113922 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113922/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113922/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113922 Building REAL300020113923 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113923' /scratch/stefan/7770410/working/building/REAL300020113923 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113923 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113923/0 /scratch/stefan/7770410/working/building/REAL300020113923 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1461) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1461 `/scratch/stefan/7770410/working/3D/1461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113923.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113923 none C=CCOC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [135, 105, 48, 46, 30, 46, 30, 30, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 8, 135, 135, 135, 105, 105, 46, 46, 46, 46, 30, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [39, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 579 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113923 none C=CCOC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 116, 109, 78, 109, 78, 78, 40, 40, 40, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 40, 201, 201, 201, 201, 201, 109, 109, 109, 109, 78, 40, 40, 40, 40, 9, 4, 4, 2, 2, 40, 40] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 846 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113923 none C=CCOC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 29, 12, 10, 6, 10, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 26, 39, 42, 42, 42, 42, 8, 8, 1, 52, 52, 52, 29, 29, 10, 10, 10, 10, 6, 1, 1, 1, 1, 8, 26, 26, 39, 39, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 11, 12, 45, 44, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 353 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113923 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113923/1 /scratch/stefan/7770410/working/building/REAL300020113923 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1462) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1462 `/scratch/stefan/7770410/working/3D/1462' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113923.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113923 none C=CCOC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [132, 103, 47, 46, 30, 46, 30, 30, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 8, 132, 132, 132, 103, 103, 46, 46, 46, 46, 30, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [39, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 564 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113923 none C=CCOC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 114, 108, 76, 108, 76, 76, 38, 38, 38, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 38, 201, 201, 201, 201, 201, 108, 108, 108, 108, 76, 38, 38, 38, 38, 8, 4, 4, 2, 2, 38, 38] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 858 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113923 none C=CCOC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 29, 11, 10, 6, 10, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 26, 39, 42, 42, 42, 42, 8, 8, 1, 52, 52, 52, 29, 29, 10, 10, 10, 10, 6, 1, 1, 1, 1, 8, 26, 26, 39, 39, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 11, 12, 45, 44, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 354 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113923 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113923 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113923/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113923/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113923 Building REAL300020113924 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113924' /scratch/stefan/7770410/working/building/REAL300020113924 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113924 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113924/0 /scratch/stefan/7770410/working/building/REAL300020113924 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1463) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1463 `/scratch/stefan/7770410/working/3D/1463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCOC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113924.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113924 none CC(C)CCOC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 71, 45, 41, 24, 41, 24, 24, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 106, 106, 106, 106, 106, 106, 106, 106, 106, 71, 71, 41, 41, 41, 41, 24, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [13, 14, 47, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 538 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113924 none CC(C)CCOC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 140, 122, 119, 82, 119, 82, 82, 39, 39, 39, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 39, 201, 201, 201, 201, 201, 201, 201, 201, 201, 140, 140, 119, 119, 119, 119, 82, 39, 39, 39, 39, 9, 5, 5, 3, 3, 39, 39] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 921 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113924 none CC(C)CCOC(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 27, 13, 11, 6, 11, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 25, 38, 39, 39, 39, 39, 8, 8, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 27, 27, 11, 11, 11, 11, 6, 1, 1, 1, 1, 8, 25, 25, 38, 38, 1, 1] 201 rigid atoms, others: [11, 44, 10, 43, 12, 13, 14, 45, 52, 46, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 348 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113924 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113924/1 /scratch/stefan/7770410/working/building/REAL300020113924 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1464) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1464 `/scratch/stefan/7770410/working/3D/1464' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCOC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113924.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113924 none CC(C)CCOC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 71, 47, 42, 24, 42, 24, 24, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 107, 107, 107, 107, 107, 107, 107, 107, 107, 71, 71, 42, 42, 42, 42, 24, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [13, 14, 47, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 540 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113924 none CC(C)CCOC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 140, 122, 118, 81, 118, 81, 81, 39, 39, 39, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 39, 201, 201, 201, 201, 201, 201, 201, 201, 201, 140, 140, 118, 118, 118, 118, 81, 39, 39, 39, 39, 9, 5, 5, 3, 3, 39, 39] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 921 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113924 none CC(C)CCOC(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 26, 13, 11, 6, 11, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 25, 38, 39, 39, 39, 39, 8, 8, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 26, 26, 11, 11, 11, 11, 6, 1, 1, 1, 1, 8, 25, 25, 38, 38, 1, 1] 201 rigid atoms, others: [11, 44, 10, 43, 12, 13, 14, 45, 52, 46, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113924 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113924 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113924/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113924/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113924 Building REAL300020113925 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113925' /scratch/stefan/7770410/working/building/REAL300020113925 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113925 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113925/0 /scratch/stefan/7770410/working/building/REAL300020113925 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1465) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1465 `/scratch/stefan/7770410/working/3D/1465' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OCC1CCCO1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113925.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113925 none CC(OCC1CCCO1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 14, 19, 29, 48, 48, 48, 48, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 24, 36, 37, 37, 37, 37, 9, 9, 1, 14, 14, 14, 14, 29, 29, 48, 48, 48, 48, 48, 48, 48, 6, 1, 1, 1, 1, 9, 24, 24, 36, 36, 1, 1] 201 rigid atoms, others: [45, 43, 44, 42, 11, 12, 13, 14, 15, 51, 52, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50]) total number of confs: 323 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113925 none CC(OCC1CCCO1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 31, 51, 63, 87, 123, 123, 123, 123, 31, 31, 9, 9, 9, 1, 1, 1, 1, 1, 5, 7, 8, 8, 8, 8, 1, 1, 9, 51, 51, 51, 51, 87, 87, 123, 123, 123, 123, 123, 123, 123, 31, 9, 9, 9, 9, 1, 5, 5, 7, 7, 9, 9] 201 rigid atoms, others: [46, 15, 16, 17, 18, 14, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 500 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113925 none CC(OCC1CCCO1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 13, 5, 1, 1, 1, 1, 1, 1, 16, 21, 21, 21, 48, 48, 48, 123, 123, 123, 176, 201, 201, 201, 201, 201, 123, 123, 48, 16, 16, 16, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 21, 48, 48, 48, 48, 123, 176, 176, 201, 201, 48, 48] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 39, 40, 35, 36, 38, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 678 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113925 none CC(OCC1CCCO1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [121, 98, 121, 127, 171, 201, 201, 201, 201, 98, 98, 38, 38, 38, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 38, 121, 121, 121, 121, 171, 171, 201, 201, 201, 201, 201, 201, 201, 98, 38, 38, 38, 38, 8, 4, 4, 2, 2, 38, 38] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 789 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113925 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113925/1 /scratch/stefan/7770410/working/building/REAL300020113925 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1466) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1466 `/scratch/stefan/7770410/working/3D/1466' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OCC1CCCO1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113925.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113925 none CC(OCC1CCCO1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 14, 19, 29, 48, 48, 48, 48, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 24, 36, 37, 37, 37, 37, 9, 9, 1, 14, 14, 14, 14, 29, 29, 48, 48, 48, 48, 48, 48, 48, 6, 1, 1, 1, 1, 9, 24, 24, 36, 36, 1, 1] 201 rigid atoms, others: [45, 43, 44, 42, 11, 12, 13, 14, 15, 51, 52, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50]) total number of confs: 323 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113925 none CC(OCC1CCCO1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 31, 52, 63, 87, 123, 123, 123, 123, 31, 31, 9, 9, 9, 1, 1, 1, 1, 1, 5, 7, 8, 8, 8, 8, 1, 1, 9, 52, 52, 52, 52, 87, 87, 123, 123, 123, 123, 123, 123, 123, 31, 9, 9, 9, 9, 1, 5, 5, 7, 7, 9, 9] 201 rigid atoms, others: [46, 15, 16, 17, 18, 14, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 504 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113925 none CC(OCC1CCCO1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 13, 5, 1, 1, 1, 1, 1, 1, 16, 21, 21, 21, 48, 48, 48, 123, 123, 123, 176, 201, 201, 201, 201, 201, 123, 123, 48, 16, 16, 16, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 21, 48, 48, 48, 48, 123, 176, 176, 201, 201, 48, 48] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 39, 40, 35, 36, 38, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 678 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113925 none CC(OCC1CCCO1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 97, 120, 126, 171, 201, 201, 201, 201, 97, 97, 37, 37, 37, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 37, 120, 120, 120, 120, 171, 171, 201, 201, 201, 201, 201, 201, 201, 97, 37, 37, 37, 37, 7, 4, 4, 2, 2, 37, 37] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 793 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113925 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113925 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113925/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113925/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113925 Building REAL300020113926 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113926' /scratch/stefan/7770410/working/building/REAL300020113926 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113926 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113926/0 /scratch/stefan/7770410/working/building/REAL300020113926 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1467) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1467 `/scratch/stefan/7770410/working/3D/1467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1) `REAL300020113926.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113926 none CCC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 24, 24, 24, 24, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 34, 43, 57, 57, 57, 57, 7, 7, 1, 24, 60, 60, 60, 60, 60, 24, 6, 1, 1, 1, 1, 7, 34, 34, 43, 43, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 389 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113926 none CCC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 51, 51, 51, 51, 25, 25, 25, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 7, 51, 115, 115, 115, 115, 115, 51, 25, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 463 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113926 none CCC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 24, 24, 24, 51, 51, 51, 108, 127, 140, 140, 140, 140, 51, 51, 24, 1, 7, 7, 7, 7, 7, 1, 7, 24, 24, 24, 24, 51, 108, 108, 127, 127, 24, 24] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 25, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 500 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113926 none CCC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 140, 140, 140, 140, 126, 126, 126, 60, 60, 60, 20, 20, 20, 6, 4, 1, 1, 1, 1, 1, 1, 20, 20, 60, 140, 201, 201, 201, 201, 201, 140, 126, 60, 60, 60, 60, 20, 6, 6, 4, 4, 60, 60] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 744 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113926 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113926/1 /scratch/stefan/7770410/working/building/REAL300020113926 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1468) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1468 `/scratch/stefan/7770410/working/3D/1468' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1) `REAL300020113926.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113926 none CCC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 24, 24, 24, 24, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 34, 43, 58, 58, 58, 58, 7, 7, 1, 24, 58, 58, 58, 58, 58, 24, 6, 1, 1, 1, 1, 7, 34, 34, 43, 43, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 385 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113926 none CCC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 51, 51, 51, 51, 24, 24, 24, 7, 7, 7, 1, 1, 1, 1, 1, 8, 10, 15, 15, 15, 15, 1, 1, 7, 51, 114, 114, 114, 114, 114, 51, 24, 7, 7, 7, 7, 1, 8, 8, 10, 10, 7, 7] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 459 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113926 none CCC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 24, 24, 24, 51, 51, 51, 101, 121, 133, 133, 133, 133, 51, 51, 24, 1, 8, 8, 8, 8, 8, 1, 7, 24, 24, 24, 24, 51, 101, 101, 121, 121, 24, 24] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 25, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 486 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113926 none CCC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 134, 134, 134, 134, 120, 120, 120, 62, 62, 62, 20, 20, 20, 6, 4, 1, 1, 1, 1, 1, 1, 20, 20, 62, 134, 201, 201, 201, 201, 201, 134, 120, 62, 62, 62, 62, 20, 6, 6, 4, 4, 62, 62] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 762 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113926 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113926 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113926/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113926/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113926 Building REAL300020113927 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113927' /scratch/stefan/7770410/working/building/REAL300020113927 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113927 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113927/0 /scratch/stefan/7770410/working/building/REAL300020113927 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1469) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1469 `/scratch/stefan/7770410/working/3D/1469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1CCC2) `REAL300020113927.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113927 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 28, 92, 92, 92, 92, 92, 92, 92, 92, 28, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 92, 92, 92, 92, 92, 92, 92, 92, 92] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 189 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113927 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 49, 49, 49, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 49, 80, 201, 201, 201, 201, 201, 201, 201, 201, 80, 49, 49, 49, 49, 11, 6, 6, 4, 4, 49, 49, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 397 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113927 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 45, 48, 48, 48, 48, 11, 11, 1, 6, 24, 24, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 11, 31, 31, 45, 45, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113927 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 24, 24, 24, 92, 92, 92, 156, 201, 201, 201, 201, 201, 92, 92, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 24, 24, 24, 24, 92, 156, 156, 201, 201, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 754 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113927 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113927/1 /scratch/stefan/7770410/working/building/REAL300020113927 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1470) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1470 `/scratch/stefan/7770410/working/3D/1470' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1CCC2) `REAL300020113927.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113927 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 28, 93, 93, 93, 93, 93, 93, 93, 93, 28, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 93, 93, 93, 93, 93, 93, 93, 93, 93] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 190 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113927 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 49, 49, 49, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 49, 80, 201, 201, 201, 201, 201, 201, 201, 201, 80, 49, 49, 49, 49, 11, 6, 6, 4, 4, 49, 49, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 398 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113927 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 45, 48, 48, 48, 48, 11, 11, 1, 6, 25, 25, 25, 25, 25, 25, 25, 25, 6, 1, 1, 1, 1, 11, 31, 31, 45, 45, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113927 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 25, 25, 25, 93, 93, 93, 156, 201, 201, 201, 201, 201, 93, 93, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 25, 25, 25, 25, 93, 156, 156, 201, 201, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 753 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113927 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113927 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113927/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113927/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113927 Building REAL300020113928 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113928' /scratch/stefan/7770410/working/building/REAL300020113928 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113928 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113928/0 /scratch/stefan/7770410/working/building/REAL300020113928 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1471) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1471 `/scratch/stefan/7770410/working/3D/1471' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113928.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113928 none COCCOCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 132, 110, 60, 48, 48, 14, 14, 14, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 133, 133, 133, 132, 132, 110, 110, 48, 48, 48, 48, 14, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 587 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113928 none COCCOCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 152, 83, 70, 70, 31, 31, 31, 24, 24, 24, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 24, 201, 201, 201, 201, 201, 152, 152, 70, 70, 70, 70, 31, 24, 24, 24, 24, 8, 4, 4, 2, 2, 24, 24] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 889 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113928 none COCCOCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 63, 50, 26, 21, 21, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 18, 29, 29, 29, 29, 29, 7, 7, 1, 70, 70, 70, 63, 63, 50, 50, 21, 21, 21, 21, 5, 1, 1, 1, 1, 7, 18, 18, 29, 29, 1, 1] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 387 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113928 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113928/1 /scratch/stefan/7770410/working/building/REAL300020113928 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1472) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1472 `/scratch/stefan/7770410/working/3D/1472' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113928.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113928 none COCCOCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 132, 110, 60, 48, 48, 14, 14, 14, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 133, 133, 133, 132, 132, 110, 110, 48, 48, 48, 48, 14, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 587 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113928 none COCCOCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 153, 83, 70, 70, 31, 31, 31, 24, 24, 24, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 24, 201, 201, 201, 201, 201, 153, 153, 70, 70, 70, 70, 31, 24, 24, 24, 24, 8, 4, 4, 2, 2, 24, 24] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 889 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113928 none COCCOCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 62, 49, 25, 20, 20, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 18, 29, 29, 29, 29, 29, 7, 7, 1, 69, 69, 69, 62, 62, 49, 49, 20, 20, 20, 20, 5, 1, 1, 1, 1, 7, 18, 18, 29, 29, 1, 1] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 384 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113928 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113928 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113928/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113928/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113928 Building REAL300020113929 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113929' /scratch/stefan/7770410/working/building/REAL300020113929 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113929 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113929/0 /scratch/stefan/7770410/working/building/REAL300020113929 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1473) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1473 `/scratch/stefan/7770410/working/3D/1473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CC=CC(F)=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113929.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113929 none CC(CC1=CC=CC(F)=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 6, 25, 37, 60, 60, 60, 60, 60, 60, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 23, 32, 32, 32, 32, 32, 12, 12, 1, 25, 25, 25, 25, 37, 37, 60, 60, 60, 60, 6, 1, 1, 1, 1, 12, 23, 23, 32, 32, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 16, 49, 50, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 320 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113929 none CC(CC1=CC=CC(F)=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 47, 110, 128, 177, 177, 177, 177, 177, 177, 47, 47, 12, 12, 12, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 12, 110, 110, 110, 110, 128, 128, 177, 177, 177, 177, 47, 12, 12, 12, 12, 1, 6, 6, 8, 8, 12, 12] 201 rigid atoms, others: [44, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 638 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113929 none CC(CC1=CC=CC(F)=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 21, 21, 21, 60, 60, 60, 177, 177, 177, 193, 201, 201, 201, 201, 201, 177, 177, 60, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 21, 60, 60, 60, 60, 177, 193, 193, 201, 201, 60, 60] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 35, 36, 38, 37] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 475 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113929 none CC(CC1=CC=CC(F)=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [155, 100, 155, 163, 201, 201, 201, 201, 201, 201, 100, 100, 43, 43, 43, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 43, 155, 155, 155, 155, 163, 163, 201, 201, 201, 201, 100, 43, 43, 43, 43, 8, 4, 4, 2, 2, 43, 43] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 673 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113929 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113929/1 /scratch/stefan/7770410/working/building/REAL300020113929 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1474) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1474 `/scratch/stefan/7770410/working/3D/1474' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CC=CC(F)=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113929.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113929/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113929 none CC(CC1=CC=CC(F)=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 6, 25, 37, 61, 61, 61, 61, 61, 61, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 23, 32, 32, 32, 32, 32, 12, 12, 1, 25, 25, 25, 25, 37, 37, 61, 61, 61, 61, 6, 1, 1, 1, 1, 12, 23, 23, 32, 32, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 16, 49, 50, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 322 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113929 none CC(CC1=CC=CC(F)=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 46, 109, 127, 177, 177, 177, 177, 177, 177, 46, 46, 12, 12, 12, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 12, 109, 109, 109, 109, 127, 127, 177, 177, 177, 177, 46, 12, 12, 12, 12, 1, 6, 6, 8, 8, 12, 12] 201 rigid atoms, others: [44, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 638 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113929 none CC(CC1=CC=CC(F)=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 22, 22, 22, 61, 61, 61, 177, 177, 177, 193, 201, 201, 201, 201, 201, 177, 177, 61, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 22, 61, 61, 61, 61, 177, 193, 193, 201, 201, 61, 61] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 35, 36, 38, 37] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 476 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113929 none CC(CC1=CC=CC(F)=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [154, 99, 154, 162, 201, 201, 201, 201, 201, 201, 99, 99, 43, 43, 43, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 43, 154, 154, 154, 154, 162, 162, 201, 201, 201, 201, 99, 43, 43, 43, 43, 8, 4, 4, 2, 2, 43, 43] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 673 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113929 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113929 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113929/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113929/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113929 Building REAL300020113930 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113930' /scratch/stefan/7770410/working/building/REAL300020113930 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113930 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113930/0 /scratch/stefan/7770410/working/building/REAL300020113930 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1475) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1475 `/scratch/stefan/7770410/working/3D/1475' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCCC1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113930.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113930 none CC1CCCCC1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 26, 26, 20, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 38, 53, 63, 63, 63, 63, 11, 11, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 20, 20, 6, 1, 1, 1, 1, 11, 38, 38, 53, 53, 1, 1] 201 rigid atoms, others: [11, 44, 10, 43, 12, 13, 14, 45, 52, 46, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 316 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113930 none CC1CCCCC1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 102, 102, 102, 94, 37, 37, 37, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 12, 12, 12, 12, 1, 1, 11, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 94, 94, 37, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11] 201 rigid atoms, others: [13, 14, 47, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 406 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113930 none CC1CCCCC1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 26, 26, 26, 102, 102, 102, 168, 201, 201, 201, 201, 201, 102, 102, 26, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 26, 26, 26, 26, 102, 168, 168, 201, 201, 26, 26] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 34, 35, 39, 36, 38, 5, 37, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 719 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113930 none CC1CCCCC1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 198, 131, 131, 131, 64, 64, 64, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 64, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 198, 198, 131, 64, 64, 64, 64, 12, 6, 6, 4, 4, 64, 64] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 741 number of broken/clashed sets: 10 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113930 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113930/1 /scratch/stefan/7770410/working/building/REAL300020113930 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1476) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1476 `/scratch/stefan/7770410/working/3D/1476' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCCC1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113930.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113930 none CC1CCCCC1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 26, 26, 20, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 37, 52, 61, 61, 61, 61, 11, 11, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 20, 20, 6, 1, 1, 1, 1, 11, 37, 37, 52, 52, 1, 1] 201 rigid atoms, others: [11, 44, 10, 43, 12, 13, 14, 45, 52, 46, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 311 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113930 none CC1CCCCC1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 102, 102, 102, 94, 37, 37, 37, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 12, 12, 12, 12, 1, 1, 11, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 94, 94, 37, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11] 201 rigid atoms, others: [13, 14, 47, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 406 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113930 none CC1CCCCC1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 26, 26, 26, 102, 102, 102, 168, 201, 201, 201, 201, 201, 102, 102, 26, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 26, 26, 26, 26, 102, 168, 168, 201, 201, 26, 26] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 34, 35, 39, 36, 38, 5, 37, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 716 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113930 none CC1CCCCC1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 198, 131, 131, 131, 63, 63, 63, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 63, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 198, 198, 131, 63, 63, 63, 63, 12, 6, 6, 4, 4, 63, 63] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 739 number of broken/clashed sets: 10 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113930 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113930 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113930/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113930/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113930 Building REAL300020113931 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113931' /scratch/stefan/7770410/working/building/REAL300020113931 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113931 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113931/0 /scratch/stefan/7770410/working/building/REAL300020113931 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1477) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1477 `/scratch/stefan/7770410/working/3D/1477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1) `REAL300020113931.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113931 none CCOC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 71, 36, 36, 36, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 12, 12, 12, 12, 1, 1, 11, 71, 83, 83, 71, 83, 83, 92, 92, 92, 92, 92, 71, 36, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 83, 83, 83, 83, 83] 201 rigid atoms, others: [40, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 424 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113931 none CCOC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 181, 105, 105, 105, 50, 50, 50, 13, 13, 13, 4, 4, 1, 1, 1, 1, 1, 1, 13, 13, 50, 181, 201, 201, 181, 201, 201, 201, 201, 201, 201, 201, 181, 105, 50, 50, 50, 50, 13, 4, 4, 4, 4, 50, 50, 201, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 849 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113931 none CCOC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 13, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 35, 48, 54, 54, 54, 54, 11, 11, 1, 13, 19, 19, 13, 19, 19, 20, 20, 20, 20, 20, 13, 6, 1, 1, 1, 1, 11, 35, 35, 48, 48, 1, 1, 19, 19, 19, 19, 19] 201 rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 39, 45, 46, 22, 38] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51]) total number of confs: 298 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113931 none CCOC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 3, 1, 3, 7, 7, 7, 19, 19, 19, 83, 83, 83, 161, 198, 201, 201, 201, 201, 83, 83, 19, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 3, 7, 19, 19, 19, 19, 83, 161, 161, 198, 198, 19, 19, 1, 1, 1, 1, 1] 201 rigid atoms, others: [3, 47, 48, 49, 50, 51, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 741 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113931 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113931/1 /scratch/stefan/7770410/working/building/REAL300020113931 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1478) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1478 `/scratch/stefan/7770410/working/3D/1478' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1) `REAL300020113931.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113931 none CCOC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 72, 36, 36, 36, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 12, 12, 12, 12, 1, 1, 11, 72, 84, 84, 72, 84, 84, 93, 93, 93, 93, 93, 72, 36, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 84, 84, 84, 84, 84] 201 rigid atoms, others: [40, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 427 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113931 none CCOC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 181, 104, 104, 104, 49, 49, 49, 12, 12, 12, 4, 4, 1, 1, 1, 1, 1, 1, 12, 12, 49, 181, 201, 201, 181, 201, 201, 201, 201, 201, 201, 201, 181, 104, 49, 49, 49, 49, 12, 4, 4, 4, 4, 49, 49, 201, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 854 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113931 none CCOC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 13, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 35, 48, 54, 54, 54, 54, 11, 11, 1, 13, 19, 19, 13, 19, 19, 20, 20, 20, 20, 20, 13, 6, 1, 1, 1, 1, 11, 35, 35, 48, 48, 1, 1, 19, 19, 19, 19, 19] 201 rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 39, 45, 46, 22, 38] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51]) total number of confs: 298 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113931 none CCOC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 3, 1, 3, 7, 7, 7, 19, 19, 19, 84, 84, 84, 161, 198, 201, 201, 201, 201, 84, 84, 19, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 3, 7, 19, 19, 19, 19, 84, 161, 161, 198, 198, 19, 19, 1, 1, 1, 1, 1] 201 rigid atoms, others: [3, 47, 48, 49, 50, 51, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 740 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113931 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113931 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113931/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113931/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113931 Building REAL300020113932 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113932' /scratch/stefan/7770410/working/building/REAL300020113932 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113932 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113932/0 /scratch/stefan/7770410/working/building/REAL300020113932 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1479) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1479 `/scratch/stefan/7770410/working/3D/1479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CC=CC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113932.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113932 none O=C(CCC1=CC=CC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 18, 22, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 9, 9, 9, 25, 39, 41, 41, 41, 41, 9, 9, 1, 18, 18, 22, 22, 33, 33, 33, 33, 6, 1, 1, 1, 1, 9, 25, 25, 39, 39, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 273 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113932 none O=C(CCC1=CC=CC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 76, 85, 111, 111, 111, 111, 111, 9, 9, 9, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 9, 76, 76, 85, 85, 111, 111, 111, 111, 27, 9, 9, 9, 9, 1, 5, 5, 7, 7, 9, 9] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 404 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113932 none O=C(CCC1=CC=CC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 10, 6, 1, 1, 1, 1, 1, 1, 1, 16, 16, 33, 33, 33, 111, 111, 111, 166, 201, 201, 201, 201, 201, 111, 111, 33, 10, 10, 6, 6, 1, 1, 1, 1, 16, 33, 33, 33, 33, 111, 166, 166, 201, 201, 33, 33] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 723 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113932 none O=C(CCC1=CC=CC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 195, 201, 201, 201, 201, 201, 201, 41, 41, 41, 9, 9, 9, 6, 4, 1, 1, 1, 1, 1, 1, 9, 9, 41, 195, 195, 201, 201, 201, 201, 201, 201, 91, 41, 41, 41, 41, 9, 6, 6, 4, 4, 41, 41] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 735 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113932 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113932/1 /scratch/stefan/7770410/working/building/REAL300020113932 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1480) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1480 `/scratch/stefan/7770410/working/3D/1480' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CC=CC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113932.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113932 none O=C(CCC1=CC=CC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 18, 22, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 9, 9, 9, 24, 38, 40, 40, 40, 40, 9, 9, 1, 18, 18, 22, 22, 33, 33, 33, 33, 6, 1, 1, 1, 1, 9, 24, 24, 38, 38, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 270 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113932 none O=C(CCC1=CC=CC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 77, 86, 112, 112, 112, 112, 112, 9, 9, 9, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 9, 77, 77, 86, 86, 112, 112, 112, 112, 27, 9, 9, 9, 9, 1, 5, 5, 7, 7, 9, 9] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 407 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113932 none O=C(CCC1=CC=CC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 10, 6, 1, 1, 1, 1, 1, 1, 1, 16, 16, 33, 33, 33, 112, 112, 112, 170, 201, 201, 201, 201, 201, 112, 112, 33, 10, 10, 6, 6, 1, 1, 1, 1, 16, 33, 33, 33, 33, 112, 170, 170, 201, 201, 33, 33] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 709 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113932 none O=C(CCC1=CC=CC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 194, 201, 201, 201, 201, 201, 201, 41, 41, 41, 9, 9, 9, 6, 4, 1, 1, 1, 1, 1, 1, 9, 9, 41, 194, 194, 201, 201, 201, 201, 201, 201, 90, 41, 41, 41, 41, 9, 6, 6, 4, 4, 41, 41] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 737 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113932 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113932 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113932/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113932/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113932 Building REAL300020113933 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113933' /scratch/stefan/7770410/working/building/REAL300020113933 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113933 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113933/0 /scratch/stefan/7770410/working/building/REAL300020113933 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1481) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1481 `/scratch/stefan/7770410/working/3D/1481' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CC=C(F)C=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113933.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113933 none CC(CC1=CC=C(F)C=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 16, 26, 26, 26, 26, 26, 26, 26, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 29, 42, 44, 44, 44, 44, 9, 9, 1, 16, 16, 16, 16, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 9, 29, 29, 42, 42, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 16, 49, 50, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 290 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113933 none CC(CC1=CC=C(F)C=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 33, 73, 108, 108, 108, 108, 108, 108, 108, 33, 33, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 73, 73, 73, 73, 108, 108, 108, 108, 108, 108, 33, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9] 201 rigid atoms, others: [44, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 501 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113933 none CC(CC1=CC=C(F)C=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 26, 26, 26, 108, 108, 108, 164, 201, 201, 201, 201, 201, 108, 108, 26, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 11, 26, 26, 26, 26, 108, 164, 164, 201, 201, 26, 26] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 8, 9, 7, 34, 35, 36, 38, 37] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 706 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113933 none CC(CC1=CC=C(F)C=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [170, 95, 170, 201, 201, 201, 201, 201, 201, 201, 95, 95, 45, 45, 45, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 45, 170, 170, 170, 170, 201, 201, 201, 201, 201, 201, 95, 45, 45, 45, 45, 12, 6, 6, 4, 4, 45, 45] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 803 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113933 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113933/1 /scratch/stefan/7770410/working/building/REAL300020113933 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1482) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1482 `/scratch/stefan/7770410/working/3D/1482' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CC=C(F)C=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113933.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113933 none CC(CC1=CC=C(F)C=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 16, 26, 26, 26, 26, 26, 26, 26, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 29, 42, 45, 45, 45, 45, 9, 9, 1, 16, 16, 16, 16, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 9, 29, 29, 42, 42, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 16, 49, 50, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 292 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113933 none CC(CC1=CC=C(F)C=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 33, 74, 109, 109, 109, 109, 109, 109, 109, 33, 33, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 74, 74, 74, 74, 109, 109, 109, 109, 109, 109, 33, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9] 201 rigid atoms, others: [44, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 507 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113933 none CC(CC1=CC=C(F)C=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 26, 26, 26, 109, 109, 109, 164, 201, 201, 201, 201, 201, 109, 109, 26, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 11, 26, 26, 26, 26, 109, 164, 164, 201, 201, 26, 26] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 8, 9, 7, 34, 35, 36, 38, 37] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 701 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113933 none CC(CC1=CC=C(F)C=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [171, 96, 171, 201, 201, 201, 201, 201, 201, 201, 96, 96, 45, 45, 45, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 45, 171, 171, 171, 171, 201, 201, 201, 201, 201, 201, 96, 45, 45, 45, 45, 12, 6, 6, 4, 4, 45, 45] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 801 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113933 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113933 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113933/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113933/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113933 Building REAL300020113934 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113934' /scratch/stefan/7770410/working/building/REAL300020113934 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113934 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113934/0 /scratch/stefan/7770410/working/building/REAL300020113934 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1483) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1483 `/scratch/stefan/7770410/working/3D/1483' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CSC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113934.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113934 none O=C(CCC1=CSC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 14, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 21, 24, 33, 33, 33, 33, 1, 1, 1, 1, 1, 8, 8, 8, 22, 34, 35, 35, 35, 35, 8, 8, 1, 21, 21, 24, 24, 33, 33, 6, 1, 1, 1, 1, 8, 22, 22, 34, 34, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 246 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113934 none O=C(CCC1=CSC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 14, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 86, 91, 107, 107, 107, 107, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 8, 8, 8, 8, 1, 1, 8, 86, 86, 91, 91, 107, 107, 25, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [37, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 373 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113934 none O=C(CCC1=CSC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 14, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 33, 33, 33, 107, 107, 107, 161, 201, 201, 201, 201, 201, 107, 107, 33, 6, 6, 4, 4, 1, 1, 17, 33, 33, 33, 33, 107, 161, 161, 201, 201, 33, 33] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 735 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113934 none O=C(CCC1=CSC=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 14, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 185, 190, 201, 201, 201, 201, 35, 35, 35, 8, 8, 8, 5, 3, 1, 1, 1, 1, 1, 1, 8, 8, 35, 185, 185, 190, 190, 201, 201, 73, 35, 35, 35, 35, 8, 5, 5, 3, 3, 35, 35] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 709 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113934 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113934/1 /scratch/stefan/7770410/working/building/REAL300020113934 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1484) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1484 `/scratch/stefan/7770410/working/3D/1484' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CSC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113934.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113934 none O=C(CCC1=CSC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 14, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 21, 24, 34, 34, 34, 34, 1, 1, 1, 1, 1, 8, 8, 8, 22, 35, 36, 36, 36, 36, 8, 8, 1, 21, 21, 24, 24, 34, 34, 6, 1, 1, 1, 1, 8, 22, 22, 35, 35, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 254 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113934 none O=C(CCC1=CSC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 14, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 87, 92, 109, 109, 109, 109, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 8, 8, 8, 8, 1, 1, 8, 87, 87, 92, 92, 109, 109, 26, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [37, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 379 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113934 none O=C(CCC1=CSC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 14, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 34, 34, 34, 109, 109, 109, 163, 201, 201, 201, 201, 201, 109, 109, 34, 6, 6, 4, 4, 1, 1, 18, 34, 34, 34, 34, 109, 163, 163, 201, 201, 34, 34] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 729 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113934 none O=C(CCC1=CSC=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 14, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 185, 190, 201, 201, 201, 201, 36, 36, 36, 8, 8, 8, 5, 3, 1, 1, 1, 1, 1, 1, 8, 8, 36, 185, 185, 190, 190, 201, 201, 73, 36, 36, 36, 36, 8, 5, 5, 3, 3, 36, 36] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 710 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113934 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113934 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113934/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113934/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113934 Building REAL300020113935 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113935' /scratch/stefan/7770410/working/building/REAL300020113935 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113935 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113935/0 /scratch/stefan/7770410/working/building/REAL300020113935 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1485) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1485 `/scratch/stefan/7770410/working/3D/1485' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=C1) `REAL300020113935.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113935 none CC1=NN(C(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 12, 6, 12, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 36, 51, 64, 64, 64, 64, 10, 10, 1, 24, 24, 24, 24, 24, 24, 12, 12, 12, 12, 6, 1, 1, 1, 1, 10, 36, 36, 51, 51, 1, 1, 24, 24, 24, 24] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 45, 46, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50]) total number of confs: 294 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113935 none CC1=NN(C(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 59, 38, 59, 38, 38, 10, 10, 10, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 10, 105, 105, 105, 105, 105, 105, 59, 59, 59, 59, 38, 10, 10, 10, 10, 1, 8, 8, 10, 10, 10, 10, 105, 105, 105, 105] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 340 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113935 none CC1=NN(C(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 24, 24, 24, 105, 105, 105, 176, 201, 201, 201, 201, 201, 105, 105, 24, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 8, 24, 24, 24, 24, 105, 176, 176, 201, 201, 24, 24, 2, 2, 2, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 50, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 708 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113935 none CC1=NN(C(C)C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 196, 147, 196, 147, 147, 64, 64, 64, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 64, 201, 201, 201, 201, 201, 201, 196, 196, 196, 196, 147, 64, 64, 64, 64, 13, 6, 6, 4, 4, 64, 64, 201, 201, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 713 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113935 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113935/1 /scratch/stefan/7770410/working/building/REAL300020113935 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1486) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1486 `/scratch/stefan/7770410/working/3D/1486' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=C1) `REAL300020113935.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113935 none CC1=NN(C(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 12, 6, 12, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 36, 51, 65, 65, 65, 65, 10, 10, 1, 23, 23, 23, 23, 23, 23, 12, 12, 12, 12, 6, 1, 1, 1, 1, 10, 36, 36, 51, 51, 1, 1, 23, 23, 23, 23] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 45, 46, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50]) total number of confs: 295 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113935 none CC1=NN(C(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 58, 38, 58, 38, 38, 10, 10, 10, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 10, 100, 100, 100, 100, 100, 100, 58, 58, 58, 58, 38, 10, 10, 10, 10, 1, 8, 8, 10, 10, 10, 10, 100, 100, 100, 100] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 327 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113935 none CC1=NN(C(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 23, 23, 23, 100, 100, 100, 175, 201, 201, 201, 201, 201, 100, 100, 23, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 8, 23, 23, 23, 23, 100, 175, 175, 201, 201, 23, 23, 2, 2, 2, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 50, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 723 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113935 none CC1=NN(C(C)C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 195, 149, 195, 149, 149, 67, 67, 67, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 67, 201, 201, 201, 201, 201, 201, 195, 195, 195, 195, 149, 67, 67, 67, 67, 14, 6, 6, 4, 4, 67, 67, 201, 201, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 697 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113935 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113935 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113935/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113935/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113935 Building REAL300020113936 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113936' /scratch/stefan/7770410/working/building/REAL300020113936 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113936 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113936/0 /scratch/stefan/7770410/working/building/REAL300020113936 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1487) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1487 `/scratch/stefan/7770410/working/3D/1487' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCC[NH+]1CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113936.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113936 none O=C(CCCC[NH+]1CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 5, 5, 5, 5, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 4, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1] 8 rigid atoms, others: [16, 12, 13, 46, 15, 48, 49, 14, 55, 56, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53, 54]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113936 none O=C(CCCC[NH+]1CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 5, 4, 4, 4, 4, 1, 3, 3, 3, 3, 4, 4] 8 rigid atoms, others: [50, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56]) total number of confs: 34 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113936 none O=C(CCCC[NH+]1CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 8 rigid atoms, others: [43, 5, 6, 7, 8, 9, 10, 11, 44, 40, 41, 39, 38, 42, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113936 none O=C(CCCC[NH+]1CCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 4, 4, 4, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 3, 3, 3, 1, 1, 4, 4] 5 rigid atoms, others: [22, 19, 20, 21, 54, 23, 24, 25, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 55, 56]) total number of confs: 18 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113936 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113936/1 /scratch/stefan/7770410/working/building/REAL300020113936 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1488) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1488 `/scratch/stefan/7770410/working/3D/1488' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCC[NH+]1CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113936.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113936 none O=C(CCCC[NH+]1CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 5, 5, 5, 5, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 4, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1] 8 rigid atoms, others: [16, 12, 13, 46, 15, 48, 49, 14, 55, 56, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53, 54]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113936 none O=C(CCCC[NH+]1CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 5, 4, 4, 4, 4, 1, 3, 3, 3, 3, 4, 4] 8 rigid atoms, others: [50, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56]) total number of confs: 34 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113936 none O=C(CCCC[NH+]1CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 8 rigid atoms, others: [43, 5, 6, 7, 8, 9, 10, 11, 44, 40, 41, 39, 38, 42, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113936 none O=C(CCCC[NH+]1CCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 4, 4, 4, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 3, 3, 3, 1, 1, 4, 4] 5 rigid atoms, others: [22, 19, 20, 21, 54, 23, 24, 25, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 55, 56]) total number of confs: 18 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113936 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113936 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113936/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113936/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113936 Building REAL300020113937 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113937' /scratch/stefan/7770410/working/building/REAL300020113937 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113937 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113937/0 /scratch/stefan/7770410/working/building/REAL300020113937 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1489) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1489 `/scratch/stefan/7770410/working/3D/1489' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1) `REAL300020113937.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113937 none CN(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 64, 36, 36, 36, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 92, 92, 92, 92, 92, 92, 92, 92, 92, 64, 64, 36, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 92, 92, 92, 92, 92] 201 rigid atoms, others: [38, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 385 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113937 none CN(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 163, 114, 114, 114, 56, 56, 56, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 56, 201, 201, 201, 201, 201, 201, 201, 201, 201, 163, 163, 114, 56, 56, 56, 56, 11, 6, 6, 4, 4, 56, 56, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 729 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113937 none CN(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 12, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 36, 50, 56, 56, 56, 56, 11, 11, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 12, 12, 6, 1, 1, 1, 1, 11, 36, 36, 50, 50, 1, 1, 17, 17, 17, 17, 17] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 43, 44, 21, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49]) total number of confs: 269 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113937 none CN(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 5, 5, 5, 5, 17, 17, 17, 92, 92, 92, 168, 201, 201, 201, 201, 201, 92, 92, 17, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 17, 17, 17, 17, 92, 168, 168, 201, 201, 17, 17, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 45, 46, 47, 48, 49, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 733 number of broken/clashed sets: 201 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113937 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113937/1 /scratch/stefan/7770410/working/building/REAL300020113937 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1490) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1490 `/scratch/stefan/7770410/working/3D/1490' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1) `REAL300020113937.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113937/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113937 none CN(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 64, 36, 36, 36, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 92, 92, 92, 92, 92, 92, 92, 92, 92, 64, 64, 36, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 92, 92, 92, 92, 92] 201 rigid atoms, others: [38, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 382 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113937 none CN(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 163, 114, 114, 114, 56, 56, 56, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 56, 201, 201, 201, 201, 201, 201, 201, 201, 201, 163, 163, 114, 56, 56, 56, 56, 11, 6, 6, 4, 4, 56, 56, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 729 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113937 none CN(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 12, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 35, 49, 55, 55, 55, 55, 11, 11, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 12, 12, 6, 1, 1, 1, 1, 11, 35, 35, 49, 49, 1, 1, 17, 17, 17, 17, 17] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 43, 44, 21, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49]) total number of confs: 266 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113937 none CN(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 5, 5, 5, 5, 17, 17, 17, 92, 92, 92, 168, 201, 201, 201, 201, 201, 92, 92, 17, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 17, 17, 17, 17, 92, 168, 168, 201, 201, 17, 17, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 45, 46, 47, 48, 49, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 736 number of broken/clashed sets: 201 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113937 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113937 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113937/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113937/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113937 Building REAL300020113938 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113938' /scratch/stefan/7770410/working/building/REAL300020113938 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113938 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113938/0 /scratch/stefan/7770410/working/building/REAL300020113938 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1491) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1491 `/scratch/stefan/7770410/working/3D/1491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)CC1=CC=CC=C1) `REAL300020113938.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113938 none CN(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 65, 31, 31, 31, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 10, 67, 81, 108, 108, 106, 108, 108, 67, 67, 67, 65, 65, 31, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 81, 81, 108, 108, 108, 108, 108] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 413 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113938 none CN(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [175, 173, 86, 86, 86, 46, 46, 46, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 46, 175, 201, 201, 201, 201, 201, 201, 175, 175, 175, 173, 173, 86, 46, 46, 46, 46, 10, 6, 6, 4, 4, 46, 46, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 777 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113938 none CN(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 16, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 30, 43, 46, 46, 46, 46, 10, 10, 1, 18, 23, 36, 36, 36, 36, 36, 18, 18, 18, 16, 16, 6, 1, 1, 1, 1, 10, 30, 30, 43, 43, 1, 1, 23, 23, 36, 36, 36, 36, 36] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 44, 45, 21, 38, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113938 none CN(CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 3, 6, 13, 17, 17, 17, 36, 36, 36, 108, 108, 108, 174, 201, 201, 201, 201, 201, 108, 108, 36, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 17, 36, 36, 36, 36, 108, 174, 174, 201, 201, 36, 36, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [48, 49, 50, 51, 52, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 726 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113938 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113938/1 /scratch/stefan/7770410/working/building/REAL300020113938 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1492) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1492 `/scratch/stefan/7770410/working/3D/1492' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)CC1=CC=CC=C1) `REAL300020113938.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113938/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113938 none CN(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 65, 31, 31, 31, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 10, 66, 80, 108, 108, 106, 108, 108, 66, 66, 66, 65, 65, 31, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 80, 80, 108, 108, 108, 108, 108] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 411 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113938 none CN(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [174, 173, 86, 86, 86, 46, 46, 46, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 46, 174, 201, 201, 201, 201, 201, 201, 174, 174, 174, 173, 173, 86, 46, 46, 46, 46, 10, 6, 6, 4, 4, 46, 46, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 779 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113938 none CN(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 16, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 29, 42, 45, 45, 45, 45, 10, 10, 1, 17, 22, 35, 35, 35, 35, 35, 17, 17, 17, 16, 16, 6, 1, 1, 1, 1, 10, 29, 29, 42, 42, 1, 1, 22, 22, 35, 35, 35, 35, 35] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 44, 45, 21, 38, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113938 none CN(CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 3, 6, 13, 16, 16, 16, 35, 35, 35, 108, 108, 108, 173, 201, 201, 201, 201, 201, 108, 108, 35, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 16, 35, 35, 35, 35, 108, 173, 173, 201, 201, 35, 35, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [48, 49, 50, 51, 52, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 725 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113938 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113938 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113938/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113938/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113938 Building REAL300020113939 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113939' /scratch/stefan/7770410/working/building/REAL300020113939 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113939 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113939/0 /scratch/stefan/7770410/working/building/REAL300020113939 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1493) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1493 `/scratch/stefan/7770410/working/3D/1493' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(NC(N)=O)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113939.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113939 none CCCCC(NC(N)=O)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 98, 94, 63, 21, 63, 72, 72, 72, 21, 21, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 98, 98, 98, 98, 98, 98, 98, 98, 98, 63, 72, 72, 72, 21, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [46, 15, 16, 17, 18, 14, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 520 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113939 none CCCCC(NC(N)=O)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [195, 201, 195, 144, 56, 144, 158, 158, 158, 56, 56, 27, 27, 27, 8, 8, 8, 3, 3, 1, 1, 1, 1, 1, 1, 8, 8, 27, 201, 201, 201, 201, 201, 201, 201, 201, 201, 144, 158, 158, 158, 56, 27, 27, 27, 27, 8, 3, 3, 3, 3, 27, 27] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 975 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113939 none CCCCC(NC(N)=O)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 34, 32, 18, 5, 18, 24, 24, 24, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 35, 35, 35, 35, 8, 8, 1, 34, 34, 34, 34, 34, 34, 34, 34, 34, 18, 24, 24, 24, 5, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1] 201 rigid atoms, others: [45, 43, 44, 42, 11, 12, 13, 14, 15, 51, 52, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50]) total number of confs: 329 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113939 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113939/1 /scratch/stefan/7770410/working/building/REAL300020113939 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1494) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1494 `/scratch/stefan/7770410/working/3D/1494' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(NC(N)=O)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113939.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113939 none CCCCC(NC(N)=O)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 98, 94, 64, 21, 64, 73, 73, 73, 21, 21, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 98, 98, 98, 98, 98, 98, 98, 98, 98, 64, 73, 73, 73, 21, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [46, 15, 16, 17, 18, 14, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 520 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113939 none CCCCC(NC(N)=O)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [195, 201, 195, 143, 56, 143, 157, 157, 157, 56, 56, 27, 27, 27, 8, 8, 8, 3, 3, 1, 1, 1, 1, 1, 1, 8, 8, 27, 201, 201, 201, 201, 201, 201, 201, 201, 201, 143, 157, 157, 157, 56, 27, 27, 27, 27, 8, 3, 3, 3, 3, 27, 27] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 978 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113939 none CCCCC(NC(N)=O)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 34, 32, 18, 5, 18, 24, 24, 24, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 35, 35, 35, 35, 8, 8, 1, 34, 34, 34, 34, 34, 34, 34, 34, 34, 18, 24, 24, 24, 5, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1] 201 rigid atoms, others: [45, 43, 44, 42, 11, 12, 13, 14, 15, 51, 52, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50]) total number of confs: 329 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113939 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113939 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113939/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113939/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113939 Building REAL300020113940 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113940' /scratch/stefan/7770410/working/building/REAL300020113940 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113940 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113940/0 /scratch/stefan/7770410/working/building/REAL300020113940 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1495) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1495 `/scratch/stefan/7770410/working/3D/1495' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020113940.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113940 none CN(C)C1=CC=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 8, 17, 8, 8, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 37, 55, 67, 67, 67, 67, 11, 11, 1, 8, 17, 17, 17, 17, 17, 17, 8, 8, 6, 1, 1, 1, 1, 11, 37, 37, 55, 55, 1, 1, 8] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48]) total number of confs: 295 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113940 none CN(C)C1=CC=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 51, 92, 51, 51, 51, 51, 47, 47, 47, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 51, 92, 92, 92, 92, 92, 92, 51, 51, 47, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 51] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 317 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113940 none CN(C)C1=CC=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 51, 51, 51, 138, 182, 201, 201, 201, 201, 51, 51, 8, 1, 5, 5, 5, 5, 5, 5, 1, 1, 3, 8, 8, 8, 8, 51, 138, 138, 182, 182, 8, 8, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 48, 35, 27] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 777 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113940 none CN(C)C1=CC=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 195, 195, 195, 67, 67, 67, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 67, 201, 201, 201, 201, 201, 201, 201, 201, 201, 195, 67, 67, 67, 67, 10, 6, 6, 4, 4, 67, 67, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 531 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113940 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113940/1 /scratch/stefan/7770410/working/building/REAL300020113940 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1496) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1496 `/scratch/stefan/7770410/working/3D/1496' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020113940.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113940/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113940 none CN(C)C1=CC=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 8, 18, 8, 8, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 37, 55, 67, 67, 67, 67, 11, 11, 1, 8, 18, 18, 18, 18, 18, 18, 8, 8, 6, 1, 1, 1, 1, 11, 37, 37, 55, 55, 1, 1, 8] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48]) total number of confs: 299 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113940 none CN(C)C1=CC=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 52, 93, 52, 52, 52, 52, 47, 47, 47, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 52, 93, 93, 93, 93, 93, 93, 52, 52, 47, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 52] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 319 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113940 none CN(C)C1=CC=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 52, 52, 52, 139, 182, 201, 201, 201, 201, 52, 52, 8, 1, 5, 5, 5, 5, 5, 5, 1, 1, 3, 8, 8, 8, 8, 52, 139, 139, 182, 182, 8, 8, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 48, 35, 27] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 772 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113940 none CN(C)C1=CC=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 194, 194, 194, 67, 67, 67, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 67, 201, 201, 201, 201, 201, 201, 201, 201, 201, 194, 67, 67, 67, 67, 10, 6, 6, 4, 4, 67, 67, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 529 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113940 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113940 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113940/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113940/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113940 Building REAL300020113941 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113941' /scratch/stefan/7770410/working/building/REAL300020113941 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113941 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113941/0 /scratch/stefan/7770410/working/building/REAL300020113941 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1497) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1497 `/scratch/stefan/7770410/working/3D/1497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCN1C=CN=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113941.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113941 none O=C(CCCN1C=CN=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 25, 22, 32, 58, 58, 58, 58, 1, 1, 1, 1, 1, 8, 8, 8, 15, 23, 23, 23, 23, 23, 8, 8, 1, 25, 25, 30, 30, 31, 31, 58, 58, 58, 5, 1, 1, 1, 1, 8, 15, 15, 23, 23, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 315 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113941 none O=C(CCCN1C=CN=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 79, 59, 89, 164, 164, 164, 164, 8, 8, 8, 1, 1, 1, 1, 1, 4, 6, 6, 6, 6, 6, 1, 1, 8, 79, 79, 87, 87, 87, 88, 164, 164, 164, 17, 8, 8, 8, 8, 1, 4, 4, 6, 6, 8, 8] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 687 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113941 none O=C(CCCN1C=CN=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 10, 6, 6, 1, 1, 1, 1, 1, 1, 32, 32, 58, 58, 58, 164, 164, 164, 184, 201, 201, 201, 201, 201, 164, 164, 58, 10, 10, 6, 6, 6, 6, 1, 1, 1, 32, 58, 58, 58, 58, 164, 184, 184, 201, 201, 58, 58] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 541 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113941 none O=C(CCCN1C=CN=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 115, 89, 117, 201, 201, 201, 201, 27, 27, 27, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 27, 115, 115, 115, 115, 115, 116, 201, 201, 201, 41, 27, 27, 27, 27, 7, 4, 4, 2, 2, 27, 27] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 783 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113941 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113941/1 /scratch/stefan/7770410/working/building/REAL300020113941 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1498) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1498 `/scratch/stefan/7770410/working/3D/1498' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCN1C=CN=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113941.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113941/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113941 none O=C(CCCN1C=CN=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 25, 22, 33, 59, 59, 59, 59, 1, 1, 1, 1, 1, 8, 8, 8, 15, 23, 23, 23, 23, 23, 8, 8, 1, 25, 25, 30, 30, 32, 31, 59, 59, 59, 5, 1, 1, 1, 1, 8, 15, 15, 23, 23, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 317 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113941 none O=C(CCCN1C=CN=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 80, 60, 91, 166, 166, 166, 166, 8, 8, 8, 1, 1, 1, 1, 1, 4, 6, 6, 6, 6, 6, 1, 1, 8, 80, 80, 88, 88, 89, 89, 166, 166, 166, 18, 8, 8, 8, 8, 1, 4, 4, 6, 6, 8, 8] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 691 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113941 none O=C(CCCN1C=CN=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 11, 7, 7, 1, 1, 1, 1, 1, 1, 33, 33, 59, 59, 59, 166, 166, 166, 186, 201, 201, 201, 201, 201, 166, 166, 59, 11, 11, 7, 7, 7, 7, 1, 1, 1, 33, 59, 59, 59, 59, 166, 186, 186, 201, 201, 59, 59] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 534 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113941 none O=C(CCCN1C=CN=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 114, 89, 116, 201, 201, 201, 201, 27, 27, 27, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 27, 114, 114, 114, 114, 114, 115, 201, 201, 201, 41, 27, 27, 27, 27, 7, 4, 4, 2, 2, 27, 27] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 775 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113941 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113941 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113941/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113941/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113941 Building REAL300020113942 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113942' /scratch/stefan/7770410/working/building/REAL300020113942 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113942 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113942/0 /scratch/stefan/7770410/working/building/REAL300020113942 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1499) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1499 `/scratch/stefan/7770410/working/3D/1499' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CS1) `REAL300020113942.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113942 none COCC1=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 17, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 26, 39, 43, 43, 43, 43, 8, 8, 1, 6, 6, 27, 27, 27, 17, 17, 6, 1, 1, 1, 1, 8, 26, 26, 39, 39, 1, 1, 6] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 250 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113942 none COCC1=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 77, 29, 29, 29, 29, 29, 29, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 8, 29, 29, 99, 99, 99, 77, 77, 29, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 29] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 361 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113942 none COCC1=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 29, 29, 29, 72, 104, 108, 108, 108, 108, 29, 29, 6, 1, 1, 9, 9, 9, 4, 4, 1, 6, 6, 6, 6, 29, 72, 72, 104, 104, 6, 6, 1] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 44, 25, 26] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 462 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113942 none COCC1=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 107, 107, 107, 107, 107, 107, 43, 43, 43, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 43, 107, 107, 201, 201, 201, 201, 201, 107, 43, 43, 43, 43, 10, 6, 6, 4, 4, 43, 43, 107] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 748 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113942 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113942/1 /scratch/stefan/7770410/working/building/REAL300020113942 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1500) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1500 `/scratch/stefan/7770410/working/3D/1500' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CS1) `REAL300020113942.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113942/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113942 none COCC1=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 17, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 25, 38, 42, 42, 42, 42, 8, 8, 1, 6, 6, 27, 27, 27, 17, 17, 6, 1, 1, 1, 1, 8, 25, 25, 38, 38, 1, 1, 6] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 247 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113942 none COCC1=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 77, 29, 29, 29, 29, 29, 29, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 8, 29, 29, 100, 100, 100, 77, 77, 29, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 29] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 363 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113942 none COCC1=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 29, 29, 29, 71, 103, 107, 107, 107, 107, 29, 29, 6, 1, 1, 9, 9, 9, 4, 4, 1, 6, 6, 6, 6, 29, 71, 71, 103, 103, 6, 6, 1] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 44, 25, 26] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 459 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113942 none COCC1=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 106, 106, 106, 106, 106, 106, 42, 42, 42, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 42, 106, 106, 201, 201, 201, 201, 201, 106, 42, 42, 42, 42, 10, 6, 6, 4, 4, 42, 42, 106] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 750 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113942 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113942 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113942/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113942/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113942 Building REAL300020113943 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113943' /scratch/stefan/7770410/working/building/REAL300020113943 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113943 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113943/0 /scratch/stefan/7770410/working/building/REAL300020113943 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1501) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1501 `/scratch/stefan/7770410/working/3D/1501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1) `REAL300020113943.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113943 none NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 9, 16, 9, 9, 9, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 42, 60, 72, 72, 72, 72, 13, 13, 1, 9, 9, 16, 16, 9, 9, 6, 1, 1, 1, 1, 13, 42, 42, 60, 60, 1, 1, 9] 201 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 309 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113943 none NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 61, 98, 61, 61, 61, 49, 49, 49, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 13, 61, 61, 98, 98, 61, 61, 49, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13, 61] 201 rigid atoms, others: [37, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 333 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113943 none NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 61, 61, 61, 132, 172, 183, 183, 183, 183, 61, 61, 9, 1, 1, 3, 3, 1, 1, 4, 9, 9, 9, 9, 61, 132, 132, 172, 172, 9, 9, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 44, 26, 27, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 688 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113943 none NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 183, 201, 183, 183, 183, 177, 177, 177, 73, 73, 73, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 73, 183, 183, 201, 201, 183, 183, 177, 73, 73, 73, 73, 13, 6, 6, 4, 4, 73, 73, 183] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 555 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113943 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113943/1 /scratch/stefan/7770410/working/building/REAL300020113943 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1502) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1502 `/scratch/stefan/7770410/working/3D/1502' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1) `REAL300020113943.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113943 none NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 9, 16, 9, 9, 9, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 42, 60, 72, 72, 72, 72, 13, 13, 1, 9, 9, 16, 16, 9, 9, 6, 1, 1, 1, 1, 13, 42, 42, 60, 60, 1, 1, 9] 201 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 309 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113943 none NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 60, 97, 60, 60, 60, 48, 48, 48, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 13, 60, 60, 97, 97, 60, 60, 48, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13, 60] 201 rigid atoms, others: [37, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 331 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113943 none NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 60, 60, 60, 132, 172, 183, 183, 183, 183, 60, 60, 9, 1, 1, 3, 3, 1, 1, 4, 9, 9, 9, 9, 60, 132, 132, 172, 172, 9, 9, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 44, 26, 27, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 690 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113943 none NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 183, 201, 183, 183, 183, 178, 178, 178, 75, 75, 75, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 75, 183, 183, 201, 201, 183, 183, 178, 75, 75, 75, 75, 13, 6, 6, 4, 4, 75, 75, 183] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 561 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113943 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113943 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113943/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113943/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113943 Building REAL300020113944 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113944' /scratch/stefan/7770410/working/building/REAL300020113944 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113944 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113944/0 /scratch/stefan/7770410/working/building/REAL300020113944 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1503) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1503 `/scratch/stefan/7770410/working/3D/1503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1) `REAL300020113944.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113944 none CC1CCC(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 42, 29, 11, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 22, 34, 34, 34, 34, 34, 8, 8, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 11, 11, 5, 1, 1, 1, 1, 8, 22, 22, 34, 34, 1, 1, 42, 42, 42, 42] 201 rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 49, 50, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 51, 52, 53, 54]) total number of confs: 253 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113944 none CC1CCC(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 109, 109, 83, 43, 19, 19, 19, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 109, 109, 109, 109, 109, 109, 109, 109, 109, 109, 109, 43, 43, 19, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 109, 109, 109, 109] 201 rigid atoms, others: [12, 44, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 357 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113944 none CC1CCC(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 9, 22, 22, 22, 42, 42, 42, 109, 109, 109, 169, 201, 201, 201, 201, 201, 109, 109, 42, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 9, 22, 42, 42, 42, 42, 109, 169, 169, 201, 201, 42, 42, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 51, 32, 34, 35, 52, 53, 54, 36, 26, 27, 5, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 738 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113944 none CC1CCC(OCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 161, 110, 54, 54, 54, 34, 34, 34, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 34, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 110, 110, 54, 34, 34, 34, 34, 9, 4, 4, 2, 2, 34, 34, 201, 201, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 669 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113944 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113944/1 /scratch/stefan/7770410/working/building/REAL300020113944 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1504) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1504 `/scratch/stefan/7770410/working/3D/1504' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1) `REAL300020113944.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113944/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113944 none CC1CCC(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 42, 29, 11, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 22, 34, 34, 34, 34, 34, 8, 8, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 11, 11, 5, 1, 1, 1, 1, 8, 22, 22, 34, 34, 1, 1, 42, 42, 42, 42] 201 rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 49, 50, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 51, 52, 53, 54]) total number of confs: 253 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113944 none CC1CCC(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 108, 82, 43, 19, 19, 19, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 108, 108, 108, 108, 108, 108, 108, 108, 108, 108, 108, 43, 43, 19, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 108, 108, 108, 108] 201 rigid atoms, others: [12, 44, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 356 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113944 none CC1CCC(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 9, 22, 22, 22, 42, 42, 42, 108, 108, 108, 169, 201, 201, 201, 201, 201, 108, 108, 42, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 9, 22, 42, 42, 42, 42, 108, 169, 169, 201, 201, 42, 42, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 51, 32, 34, 35, 52, 53, 54, 36, 26, 27, 5, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 742 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113944 none CC1CCC(OCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 161, 111, 55, 55, 55, 35, 35, 35, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 35, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 111, 111, 55, 35, 35, 35, 35, 9, 4, 4, 2, 2, 35, 35, 201, 201, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 669 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113944 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113944 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113944/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113944/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113944 Building REAL300020113945 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113945' /scratch/stefan/7770410/working/building/REAL300020113945 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113945 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113945/0 /scratch/stefan/7770410/working/building/REAL300020113945 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1505) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1505 `/scratch/stefan/7770410/working/3D/1505' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CSC(C2CC2)=N1) `REAL300020113945.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113945 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CSC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 51, 54, 54, 54, 54, 128, 128, 54, 51, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 54, 128, 128, 128, 128, 128] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 403 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113945 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CSC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 9, 12, 12, 30, 30, 30, 128, 128, 128, 188, 201, 201, 201, 201, 201, 128, 128, 30, 9, 9, 9, 1, 1, 1, 1, 9, 12, 30, 30, 30, 30, 128, 188, 188, 201, 201, 30, 30, 9, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 591 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113945 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CSC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [177, 177, 66, 66, 66, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 66, 177, 179, 179, 179, 179, 201, 201, 179, 177, 66, 66, 66, 66, 10, 6, 6, 4, 4, 66, 66, 179, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 579 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113945 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CSC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 42, 60, 65, 65, 65, 65, 13, 13, 1, 6, 8, 8, 8, 8, 30, 30, 8, 6, 1, 1, 1, 1, 13, 42, 42, 60, 60, 1, 1, 8, 30, 30, 30, 30, 30] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 321 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113945 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CSC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 54, 54, 54, 136, 172, 177, 177, 177, 177, 54, 54, 8, 1, 1, 1, 1, 1, 9, 9, 1, 3, 8, 8, 8, 8, 54, 136, 136, 172, 172, 8, 8, 1, 9, 9, 9, 9, 9] 201 rigid atoms, others: [1, 39, 19, 20, 21, 22, 23, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 672 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113945 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113945/1 /scratch/stefan/7770410/working/building/REAL300020113945 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1506) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1506 `/scratch/stefan/7770410/working/3D/1506' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CSC(C2CC2)=N1) `REAL300020113945.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113945 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CSC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 51, 54, 54, 54, 54, 128, 128, 54, 51, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 54, 128, 128, 128, 128, 128] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 403 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113945 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CSC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 9, 12, 12, 30, 30, 30, 128, 128, 128, 188, 201, 201, 201, 201, 201, 128, 128, 30, 9, 9, 9, 1, 1, 1, 1, 9, 12, 30, 30, 30, 30, 128, 188, 188, 201, 201, 30, 30, 9, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 591 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113945 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CSC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [177, 177, 66, 66, 66, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 66, 177, 179, 179, 179, 179, 201, 201, 179, 177, 66, 66, 66, 66, 10, 6, 6, 4, 4, 66, 66, 179, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 579 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113945 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CSC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 42, 60, 65, 65, 65, 65, 13, 13, 1, 6, 8, 8, 8, 8, 30, 30, 8, 6, 1, 1, 1, 1, 13, 42, 42, 60, 60, 1, 1, 8, 30, 30, 30, 30, 30] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 321 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113945 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CSC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 54, 54, 54, 136, 172, 177, 177, 177, 177, 54, 54, 8, 1, 1, 1, 1, 1, 9, 9, 1, 3, 8, 8, 8, 8, 54, 136, 136, 172, 172, 8, 8, 1, 9, 9, 9, 9, 9] 201 rigid atoms, others: [1, 39, 19, 20, 21, 22, 23, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 672 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113945 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113945 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113945/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113945/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113945 Building REAL300020113946 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113946' /scratch/stefan/7770410/working/building/REAL300020113946 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113946 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113946/0 /scratch/stefan/7770410/working/building/REAL300020113946 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1507) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1507 `/scratch/stefan/7770410/working/3D/1507' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1) `REAL300020113946.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113946 none CCN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 8, 20, 5, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 37, 37, 37, 37, 8, 8, 1, 12, 12, 20, 20, 20, 20, 20, 20, 20, 20, 12, 12, 5, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1, 12, 12] 201 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 49, 50, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 51, 52]) total number of confs: 219 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113946 none CCN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 32, 95, 18, 58, 58, 18, 18, 18, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 8, 58, 58, 95, 95, 95, 95, 95, 95, 95, 95, 58, 58, 18, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8, 58, 58] 201 rigid atoms, others: [44, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 408 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113946 none CCN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 58, 58, 58, 138, 196, 201, 201, 201, 201, 58, 58, 12, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 5, 12, 12, 12, 12, 58, 138, 138, 196, 196, 12, 12, 1, 1] 201 rigid atoms, others: [2, 27, 4, 5, 6, 7, 8, 51, 52, 38, 28, 37] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 839 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113946 none CCN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 118, 201, 65, 201, 201, 65, 65, 65, 41, 41, 41, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 41, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 65, 41, 41, 41, 41, 11, 6, 6, 4, 4, 41, 41, 201, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 1058 number of broken/clashed sets: 201 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113946 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113946/1 /scratch/stefan/7770410/working/building/REAL300020113946 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1508) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1508 `/scratch/stefan/7770410/working/3D/1508' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1) `REAL300020113946.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113946/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113946 none CCN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 8, 20, 5, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 37, 37, 37, 37, 8, 8, 1, 12, 12, 20, 20, 20, 20, 20, 20, 20, 20, 12, 12, 5, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1, 12, 12] 201 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 49, 50, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 51, 52]) total number of confs: 219 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113946 none CCN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 32, 95, 18, 58, 58, 18, 18, 18, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 8, 58, 58, 95, 95, 95, 95, 95, 95, 95, 95, 58, 58, 18, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8, 58, 58] 201 rigid atoms, others: [44, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 408 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113946 none CCN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 58, 58, 58, 138, 196, 201, 201, 201, 201, 58, 58, 12, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 5, 12, 12, 12, 12, 58, 138, 138, 196, 196, 12, 12, 1, 1] 201 rigid atoms, others: [2, 27, 4, 5, 6, 7, 8, 51, 52, 38, 28, 37] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 839 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113946 none CCN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 117, 201, 64, 201, 201, 64, 64, 64, 40, 40, 40, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 40, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 64, 40, 40, 40, 40, 10, 6, 6, 4, 4, 40, 40, 201, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 1062 number of broken/clashed sets: 201 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113946 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113946 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113946/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113946/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113946 Building REAL300020113947 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113947' /scratch/stefan/7770410/working/building/REAL300020113947 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113947 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113947/0 /scratch/stefan/7770410/working/building/REAL300020113947 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1509) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1509 `/scratch/stefan/7770410/working/3D/1509' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113947.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113947 none CC(C)OCCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [131, 105, 131, 65, 61, 56, 21, 21, 21, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 8, 131, 131, 131, 131, 131, 131, 131, 63, 63, 65, 65, 56, 56, 21, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [12, 44, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 537 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113947 none CC(C)OCCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 182, 201, 133, 127, 133, 68, 68, 68, 38, 38, 38, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 38, 201, 201, 201, 201, 201, 201, 201, 129, 131, 133, 133, 133, 133, 68, 38, 38, 38, 38, 10, 6, 6, 4, 4, 38, 38] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 740 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113947 none CC(C)OCCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 48, 64, 25, 23, 20, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 23, 26, 29, 29, 29, 29, 8, 8, 1, 64, 64, 64, 64, 64, 64, 64, 24, 24, 25, 25, 20, 20, 6, 1, 1, 1, 1, 8, 23, 23, 26, 26, 1, 1] 201 rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 49, 50, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113947 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113947/1 /scratch/stefan/7770410/working/building/REAL300020113947 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1510) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1510 `/scratch/stefan/7770410/working/3D/1510' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113947.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113947/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113947 none CC(C)OCCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [131, 106, 131, 66, 62, 57, 22, 22, 22, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 8, 131, 131, 131, 131, 131, 131, 131, 64, 64, 66, 66, 57, 57, 22, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [12, 44, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 533 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113947 none CC(C)OCCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 182, 201, 133, 127, 133, 68, 68, 68, 38, 38, 38, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 38, 201, 201, 201, 201, 201, 201, 201, 129, 131, 133, 133, 133, 133, 68, 38, 38, 38, 38, 10, 6, 6, 4, 4, 38, 38] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 740 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113947 none CC(C)OCCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 48, 63, 25, 23, 20, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 23, 26, 30, 30, 30, 30, 8, 8, 1, 63, 63, 63, 63, 63, 63, 63, 24, 24, 25, 25, 20, 20, 6, 1, 1, 1, 1, 8, 23, 23, 26, 26, 1, 1] 201 rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 49, 50, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 323 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113947 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113947 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113947/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113947/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113947 Building REAL300020113948 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113948' /scratch/stefan/7770410/working/building/REAL300020113948 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113948 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113948/0 /scratch/stefan/7770410/working/building/REAL300020113948 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1511) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1511 `/scratch/stefan/7770410/working/3D/1511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113948.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113948 none NC(=O)CCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [136, 121, 136, 82, 101, 23, 23, 23, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 136, 136, 109, 109, 116, 116, 101, 101, 23, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 711 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113948 none NC(=O)CCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 158, 185, 63, 63, 63, 33, 33, 33, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 33, 201, 201, 185, 184, 195, 195, 185, 185, 63, 33, 33, 33, 33, 7, 4, 4, 2, 2, 33, 33] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 954 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113948 none NC(=O)CCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 41, 58, 26, 25, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 19, 31, 31, 31, 31, 31, 7, 7, 1, 58, 58, 37, 36, 35, 35, 25, 25, 6, 1, 1, 1, 1, 7, 19, 19, 31, 31, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 394 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113948 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113948/1 /scratch/stefan/7770410/working/building/REAL300020113948 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1512) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1512 `/scratch/stefan/7770410/working/3D/1512' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113948.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113948 none NC(=O)CCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [135, 120, 135, 80, 100, 23, 23, 23, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 135, 135, 108, 107, 115, 115, 100, 100, 23, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 712 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113948 none NC(=O)CCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 157, 185, 63, 63, 63, 33, 33, 33, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 33, 201, 201, 184, 184, 195, 195, 185, 185, 63, 33, 33, 33, 33, 7, 4, 4, 2, 2, 33, 33] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 959 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113948 none NC(=O)CCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 40, 57, 25, 25, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 19, 31, 31, 31, 31, 31, 7, 7, 1, 57, 57, 36, 35, 34, 34, 25, 25, 6, 1, 1, 1, 1, 7, 19, 19, 31, 31, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 389 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113948 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113948 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113948/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113948/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113948 Building REAL300020113949 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113949' /scratch/stefan/7770410/working/building/REAL300020113949 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113949 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113949/0 /scratch/stefan/7770410/working/building/REAL300020113949 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1513) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1513 `/scratch/stefan/7770410/working/3D/1513' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+]1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1) `REAL300020113949.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113949 none C[NH+]1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 31, 31, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 32, 32, 32, 32, 32, 32, 13, 13, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 1, 1, 1, 1, 13, 32, 32, 32, 32, 1, 1, 31, 31, 31, 31] 136 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 45, 46, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50]) total number of confs: 179 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113949 none C[NH+]1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 119, 119, 119, 37, 37, 37, 13, 13, 13, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 13, 119, 119, 119, 119, 119, 119, 119, 119, 119, 119, 37, 13, 13, 13, 13, 1, 5, 5, 5, 5, 13, 13, 119, 119, 119, 119] 136 rigid atoms, others: [40, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 332 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113949 none C[NH+]1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 31, 31, 31, 119, 119, 119, 136, 136, 136, 136, 136, 136, 119, 119, 31, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 10, 31, 31, 31, 31, 119, 136, 136, 136, 136, 31, 31, 1, 1, 1, 1] 136 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 47, 33, 49, 50, 48, 25, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 298 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113949 none C[NH+]1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 134, 134, 134, 63, 63, 63, 30, 30, 30, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 30, 134, 134, 134, 134, 134, 134, 134, 134, 134, 134, 63, 30, 30, 30, 30, 5, 3, 3, 1, 1, 30, 30, 134, 134, 134, 134] 134 rigid atoms, others: [43, 44, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50]) total number of confs: 396 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113949 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113949/1 /scratch/stefan/7770410/working/building/REAL300020113949 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1514) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1514 `/scratch/stefan/7770410/working/3D/1514' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+]1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1) `REAL300020113949.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113949/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113949 none C[NH+]1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 30, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 32, 32, 32, 32, 32, 32, 13, 13, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 6, 1, 1, 1, 1, 13, 32, 32, 32, 32, 1, 1, 30, 30, 30, 30] 135 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 45, 46, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50]) total number of confs: 177 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113949 none C[NH+]1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 118, 118, 36, 36, 36, 13, 13, 13, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 13, 118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 36, 13, 13, 13, 13, 1, 5, 5, 5, 5, 13, 13, 118, 118, 118, 118] 135 rigid atoms, others: [40, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 330 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113949 none C[NH+]1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 30, 30, 30, 118, 118, 118, 135, 135, 135, 135, 135, 135, 118, 118, 30, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 10, 30, 30, 30, 30, 118, 135, 135, 135, 135, 30, 30, 1, 1, 1, 1] 135 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 47, 33, 49, 50, 48, 25, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 296 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113949 none C[NH+]1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 133, 133, 133, 62, 62, 62, 30, 30, 30, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 30, 133, 133, 133, 133, 133, 133, 133, 133, 133, 133, 62, 30, 30, 30, 30, 5, 3, 3, 1, 1, 30, 30, 133, 133, 133, 133] 133 rigid atoms, others: [43, 44, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50]) total number of confs: 394 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113949 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113949 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113949/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113949/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113949 Building REAL300020113950 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113950' /scratch/stefan/7770410/working/building/REAL300020113950 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113950 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113950/0 /scratch/stefan/7770410/working/building/REAL300020113950 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1515) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1515 `/scratch/stefan/7770410/working/3D/1515' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1) `REAL300020113950.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113950 none NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 44, 62, 72, 72, 72, 72, 11, 11, 1, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 11, 44, 44, 62, 62, 1, 1, 16] 201 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 292 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113950 none NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 98, 98, 98, 37, 37, 37, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 98, 98, 98, 98, 98, 98, 37, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 98] 201 rigid atoms, others: [37, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 225 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113950 none NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 98, 98, 98, 179, 201, 201, 201, 201, 201, 98, 98, 16, 1, 1, 2, 2, 1, 1, 5, 16, 16, 16, 16, 98, 179, 179, 201, 201, 16, 16, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 44, 26, 27, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 678 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113950 none NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 140, 140, 140, 71, 71, 71, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 71, 201, 201, 201, 201, 201, 201, 140, 71, 71, 71, 71, 12, 6, 6, 4, 4, 71, 71, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 526 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113950 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113950/1 /scratch/stefan/7770410/working/building/REAL300020113950 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1516) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1516 `/scratch/stefan/7770410/working/3D/1516' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1) `REAL300020113950.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113950 none NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 44, 62, 71, 71, 71, 71, 11, 11, 1, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 11, 44, 44, 62, 62, 1, 1, 16] 201 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 290 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113950 none NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 98, 98, 98, 37, 37, 37, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 98, 98, 98, 98, 98, 98, 37, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 98] 201 rigid atoms, others: [37, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 225 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113950 none NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 98, 98, 98, 179, 201, 201, 201, 201, 201, 98, 98, 16, 1, 1, 2, 2, 1, 1, 5, 16, 16, 16, 16, 98, 179, 179, 201, 201, 16, 16, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 44, 26, 27, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 678 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113950 none NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 140, 140, 140, 71, 71, 71, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 71, 201, 201, 201, 201, 201, 201, 140, 71, 71, 71, 71, 12, 6, 6, 4, 4, 71, 71, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 526 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113950 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113950 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113950/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113950/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113950 Building REAL300020113951 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113951' /scratch/stefan/7770410/working/building/REAL300020113951 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113951 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113951/0 /scratch/stefan/7770410/working/building/REAL300020113951 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1517) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1517 `/scratch/stefan/7770410/working/3D/1517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1COC2=CC=CC=C21) `REAL300020113951.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113951 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1COC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 12, 48, 107, 107, 107, 107, 107, 107, 107, 107, 48, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 107, 107, 107, 107, 107, 107, 107] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 342 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113951 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1COC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [159, 159, 80, 80, 80, 16, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 80, 159, 201, 201, 201, 201, 201, 201, 201, 201, 159, 80, 80, 80, 80, 16, 6, 6, 4, 4, 80, 80, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 568 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113951 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1COC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 46, 64, 80, 80, 80, 80, 12, 12, 1, 6, 25, 25, 25, 25, 25, 25, 25, 25, 6, 1, 1, 1, 1, 12, 46, 46, 64, 64, 1, 1, 25, 25, 25, 25, 25, 25, 25] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113951 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1COC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 25, 25, 25, 107, 107, 107, 173, 201, 201, 201, 201, 201, 107, 107, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 25, 25, 25, 25, 107, 173, 173, 201, 201, 25, 25, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 662 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113951 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113951/1 /scratch/stefan/7770410/working/building/REAL300020113951 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1518) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1518 `/scratch/stefan/7770410/working/3D/1518' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1COC2=CC=CC=C21) `REAL300020113951.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113951 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1COC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 12, 48, 107, 107, 107, 107, 107, 107, 107, 107, 48, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 107, 107, 107, 107, 107, 107, 107] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 342 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113951 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1COC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [159, 159, 80, 80, 80, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 80, 159, 201, 201, 201, 201, 201, 201, 201, 201, 159, 80, 80, 80, 80, 17, 6, 6, 4, 4, 80, 80, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 565 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113951 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1COC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 46, 64, 80, 80, 80, 80, 12, 12, 1, 6, 25, 25, 25, 25, 25, 25, 25, 25, 6, 1, 1, 1, 1, 12, 46, 46, 64, 64, 1, 1, 25, 25, 25, 25, 25, 25, 25] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113951 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1COC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 25, 25, 25, 107, 107, 107, 173, 201, 201, 201, 201, 201, 107, 107, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 25, 25, 25, 25, 107, 173, 173, 201, 201, 25, 25, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 662 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113951 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113951 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113951/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113951/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113951 Building REAL300020113952 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113952' /scratch/stefan/7770410/working/building/REAL300020113952 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113952 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113952/0 /scratch/stefan/7770410/working/building/REAL300020113952 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1519) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1519 `/scratch/stefan/7770410/working/3D/1519' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=COC2=CC=CC=C12) `REAL300020113952.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113952 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=COC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 35, 98, 98, 98, 98, 98, 98, 98, 98, 35, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 98, 98, 98, 98, 98] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 209 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113952 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=COC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 56, 56, 56, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 56, 115, 201, 201, 201, 201, 201, 201, 201, 201, 115, 56, 56, 56, 56, 11, 6, 6, 4, 4, 56, 56, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 469 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113952 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=COC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 48, 54, 54, 54, 54, 11, 11, 1, 6, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 33, 33, 48, 48, 1, 1, 22, 22, 22, 22, 22] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113952 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=COC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 22, 22, 22, 98, 98, 98, 158, 201, 201, 201, 201, 201, 98, 98, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 22, 22, 22, 22, 98, 158, 158, 201, 201, 22, 22, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 719 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113952 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113952/1 /scratch/stefan/7770410/working/building/REAL300020113952 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1520) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1520 `/scratch/stefan/7770410/working/3D/1520' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=COC2=CC=CC=C12) `REAL300020113952.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113952 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=COC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 34, 98, 98, 98, 98, 98, 98, 98, 98, 34, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 98, 98, 98, 98, 98] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 208 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113952 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=COC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 55, 55, 55, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 55, 115, 201, 201, 201, 201, 201, 201, 201, 201, 115, 55, 55, 55, 55, 10, 6, 6, 4, 4, 55, 55, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 468 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113952 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=COC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 48, 55, 55, 55, 55, 11, 11, 1, 6, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 33, 33, 48, 48, 1, 1, 22, 22, 22, 22, 22] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113952 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=COC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 22, 22, 22, 98, 98, 98, 158, 201, 201, 201, 201, 201, 98, 98, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 22, 22, 22, 22, 98, 158, 158, 201, 201, 22, 22, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 719 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113952 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113952 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113952/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113952/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113952 Building REAL300020113953 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113953' /scratch/stefan/7770410/working/building/REAL300020113953 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113953 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113953/0 /scratch/stefan/7770410/working/building/REAL300020113953 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1521) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1521 `/scratch/stefan/7770410/working/3D/1521' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1C1CC1) `REAL300020113953.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113953 none CN1N=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 29, 42, 43, 43, 43, 43, 11, 11, 1, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 11, 29, 29, 42, 42, 1, 1, 21, 21, 21, 21, 21] 201 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48]) total number of confs: 199 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113953 none CN1N=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 7, 7, 7, 21, 21, 21, 90, 90, 90, 158, 201, 201, 201, 201, 201, 90, 90, 21, 1, 1, 1, 1, 3, 3, 3, 3, 7, 21, 21, 21, 21, 90, 158, 158, 201, 201, 21, 21, 1, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 48, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 751 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113953 none CN1N=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 90, 32, 32, 32, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 90, 90, 90, 90, 90, 90, 90, 90, 32, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 90, 90, 90, 90, 90] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 192 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113953 none CN1N=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 21, 21, 90, 90, 90, 158, 201, 201, 201, 201, 201, 90, 90, 21, 1, 1, 3, 3, 2, 2, 2, 1, 7, 21, 21, 21, 21, 90, 158, 158, 201, 201, 21, 21, 3, 3, 3, 3, 3] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 25, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 762 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113953 none CN1N=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 89, 89, 89, 43, 43, 43, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 43, 201, 201, 201, 201, 201, 201, 201, 201, 89, 43, 43, 43, 43, 9, 5, 5, 3, 3, 43, 43, 201, 201, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 420 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113953 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113953/1 /scratch/stefan/7770410/working/building/REAL300020113953 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1522) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1522 `/scratch/stefan/7770410/working/3D/1522' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1C1CC1) `REAL300020113953.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113953/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113953 none CN1N=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 29, 42, 43, 43, 43, 43, 11, 11, 1, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 11, 29, 29, 42, 42, 1, 1, 21, 21, 21, 21, 21] 201 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48]) total number of confs: 199 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113953 none CN1N=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 7, 7, 7, 21, 21, 21, 90, 90, 90, 158, 201, 201, 201, 201, 201, 90, 90, 21, 1, 1, 1, 1, 3, 3, 3, 3, 7, 21, 21, 21, 21, 90, 158, 158, 201, 201, 21, 21, 1, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 48, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 751 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113953 none CN1N=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 90, 32, 32, 32, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 90, 90, 90, 90, 90, 90, 90, 90, 32, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 90, 90, 90, 90, 90] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 192 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113953 none CN1N=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 21, 21, 90, 90, 90, 158, 201, 201, 201, 201, 201, 90, 90, 21, 1, 1, 3, 3, 2, 2, 2, 1, 7, 21, 21, 21, 21, 90, 158, 158, 201, 201, 21, 21, 3, 3, 3, 3, 3] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 25, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 762 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113953 none CN1N=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 89, 89, 89, 44, 44, 44, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 44, 201, 201, 201, 201, 201, 201, 201, 201, 89, 44, 44, 44, 44, 10, 5, 5, 3, 3, 44, 44, 201, 201, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 419 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113953 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113953 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113953/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113953/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113953 Building REAL300020113954 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113954' /scratch/stefan/7770410/working/building/REAL300020113954 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113954 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113954/0 /scratch/stefan/7770410/working/building/REAL300020113954 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1523) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1523 `/scratch/stefan/7770410/working/3D/1523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COCCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113954.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113954 none O=C(COCCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 16, 30, 37, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 35, 35, 35, 35, 8, 8, 1, 16, 16, 37, 37, 48, 48, 48, 48, 48, 48, 48, 6, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 310 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113954 none O=C(COCCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 61, 77, 85, 109, 109, 109, 109, 109, 109, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 61, 61, 85, 85, 109, 109, 109, 109, 109, 109, 109, 24, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 470 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113954 none O=C(COCCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 22, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 48, 48, 48, 109, 109, 109, 176, 201, 201, 201, 201, 201, 109, 109, 48, 22, 22, 3, 3, 1, 1, 1, 1, 1, 1, 1, 29, 48, 48, 48, 48, 109, 176, 176, 201, 201, 48, 48] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 36, 38, 39, 37] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 765 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113954 none O=C(COCCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 135, 163, 168, 201, 201, 201, 201, 201, 201, 39, 39, 39, 10, 10, 10, 6, 3, 1, 1, 1, 1, 1, 1, 10, 10, 39, 135, 135, 168, 168, 201, 201, 201, 201, 201, 201, 201, 60, 39, 39, 39, 39, 10, 6, 6, 3, 3, 39, 39] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 799 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113954 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113954/1 /scratch/stefan/7770410/working/building/REAL300020113954 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1524) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1524 `/scratch/stefan/7770410/working/3D/1524' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COCCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113954.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113954/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113954 none O=C(COCCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 16, 30, 36, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 35, 35, 35, 35, 8, 8, 1, 16, 16, 36, 36, 47, 47, 47, 47, 47, 47, 47, 6, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 307 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113954 none O=C(COCCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 61, 78, 85, 110, 110, 110, 110, 110, 110, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 61, 61, 85, 85, 110, 110, 110, 110, 110, 110, 110, 24, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 475 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113954 none O=C(COCCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 22, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 47, 47, 47, 110, 110, 110, 175, 201, 201, 201, 201, 201, 110, 110, 47, 22, 22, 3, 3, 1, 1, 1, 1, 1, 1, 1, 29, 47, 47, 47, 47, 110, 175, 175, 201, 201, 47, 47] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 36, 38, 39, 37] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 761 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113954 none O=C(COCCC1=CC=CC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 136, 164, 169, 201, 201, 201, 201, 201, 201, 39, 39, 39, 10, 10, 10, 6, 3, 1, 1, 1, 1, 1, 1, 10, 10, 39, 136, 136, 169, 169, 201, 201, 201, 201, 201, 201, 201, 60, 39, 39, 39, 39, 10, 6, 6, 3, 3, 39, 39] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 796 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113954 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113954 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113954/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113954/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113954 Building REAL300020113955 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113955' /scratch/stefan/7770410/working/building/REAL300020113955 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113955 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113955/0 /scratch/stefan/7770410/working/building/REAL300020113955 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1525) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1525 `/scratch/stefan/7770410/working/3D/1525' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1C1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1) `REAL300020113955.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113955 none CC1=CC=CC=C1C1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 2, 3, 3, 1, 1, 1, 9, 9, 9, 36, 36, 36, 168, 168, 168, 187, 201, 201, 201, 201, 201, 168, 168, 36, 1, 1, 3, 3, 3, 3, 2, 3, 3, 9, 36, 36, 36, 36, 168, 187, 187, 201, 201, 36, 36, 1, 1, 1, 1] 201 rigid atoms, others: [6, 7, 8, 48, 49, 50, 51, 27, 28] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 453 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113955 none CC1=CC=CC=C1C1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 83, 83, 83, 29, 29, 29, 6, 6, 6, 4, 2, 1, 1, 1, 1, 1, 1, 6, 6, 29, 201, 201, 201, 201, 201, 201, 201, 201, 201, 83, 29, 29, 29, 29, 6, 4, 4, 2, 2, 29, 29, 201, 201, 201, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 567 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113955 none CC1=CC=CC=C1C1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 20, 27, 27, 27, 27, 27, 13, 13, 1, 36, 36, 36, 36, 36, 36, 36, 36, 36, 6, 1, 1, 1, 1, 13, 20, 20, 27, 27, 1, 1, 36, 36, 36, 36] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113955 none CC1=CC=CC=C1C1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 11, 11, 11, 36, 36, 36, 168, 168, 168, 187, 201, 201, 201, 201, 201, 168, 168, 36, 3, 3, 2, 2, 2, 1, 1, 1, 1, 11, 36, 36, 36, 36, 168, 187, 187, 201, 201, 36, 36, 3, 3, 3, 3] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 34, 35, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 457 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113955 none CC1=CC=CC=C1C1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [168, 168, 168, 168, 168, 168, 168, 55, 55, 55, 13, 13, 13, 1, 1, 1, 1, 1, 4, 6, 6, 6, 6, 6, 1, 1, 13, 168, 168, 168, 168, 168, 168, 168, 168, 168, 55, 13, 13, 13, 13, 1, 4, 4, 6, 6, 13, 13, 168, 168, 168, 168] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 469 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113955 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113955/1 /scratch/stefan/7770410/working/building/REAL300020113955 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1526) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1526 `/scratch/stefan/7770410/working/3D/1526' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1C1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1) `REAL300020113955.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113955/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113955 none CC1=CC=CC=C1C1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 2, 3, 3, 1, 1, 1, 9, 9, 9, 36, 36, 36, 168, 168, 168, 187, 201, 201, 201, 201, 201, 168, 168, 36, 1, 1, 3, 3, 3, 3, 2, 3, 3, 9, 36, 36, 36, 36, 168, 187, 187, 201, 201, 36, 36, 1, 1, 1, 1] 201 rigid atoms, others: [6, 7, 8, 48, 49, 50, 51, 27, 28] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 453 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113955 none CC1=CC=CC=C1C1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 82, 82, 82, 29, 29, 29, 6, 6, 6, 4, 2, 1, 1, 1, 1, 1, 1, 6, 6, 29, 201, 201, 201, 201, 201, 201, 201, 201, 201, 82, 29, 29, 29, 29, 6, 4, 4, 2, 2, 29, 29, 201, 201, 201, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 569 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113955 none CC1=CC=CC=C1C1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 20, 27, 27, 27, 27, 27, 13, 13, 1, 36, 36, 36, 36, 36, 36, 36, 36, 36, 6, 1, 1, 1, 1, 13, 20, 20, 27, 27, 1, 1, 36, 36, 36, 36] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113955 none CC1=CC=CC=C1C1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 11, 11, 11, 36, 36, 36, 168, 168, 168, 187, 201, 201, 201, 201, 201, 168, 168, 36, 3, 3, 2, 2, 2, 1, 1, 1, 1, 11, 36, 36, 36, 36, 168, 187, 187, 201, 201, 36, 36, 3, 3, 3, 3] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 34, 35, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 457 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113955 none CC1=CC=CC=C1C1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [168, 168, 168, 168, 168, 168, 168, 55, 55, 55, 13, 13, 13, 1, 1, 1, 1, 1, 4, 6, 6, 6, 6, 6, 1, 1, 13, 168, 168, 168, 168, 168, 168, 168, 168, 168, 55, 13, 13, 13, 13, 1, 4, 4, 6, 6, 13, 13, 168, 168, 168, 168] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 469 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113955 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113955 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113955/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113955/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113955 Building REAL300020113956 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113956' /scratch/stefan/7770410/working/building/REAL300020113956 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113956 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113956/0 /scratch/stefan/7770410/working/building/REAL300020113956 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1527) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1527 `/scratch/stefan/7770410/working/3D/1527' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)N1CCC[C@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113956.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113956 none NC(=O)N1CCC[C@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 25, 51, 25, 25, 25, 25, 6, 25, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 26, 34, 34, 34, 34, 34, 13, 13, 1, 51, 51, 25, 25, 25, 25, 25, 25, 6, 1, 1, 1, 1, 13, 26, 26, 34, 34, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 268 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113956 none NC(=O)N1CCC[C@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [178, 139, 178, 139, 139, 139, 139, 61, 139, 61, 61, 13, 13, 13, 1, 1, 1, 1, 1, 7, 9, 9, 9, 9, 9, 1, 1, 13, 178, 178, 139, 139, 139, 139, 139, 139, 61, 13, 13, 13, 13, 1, 7, 7, 9, 9, 13, 13] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 576 number of broken/clashed sets: 15 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113956 none NC(=O)N1CCC[C@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 25, 25, 25, 139, 139, 139, 166, 181, 181, 181, 181, 181, 139, 139, 25, 5, 5, 1, 1, 1, 1, 1, 1, 8, 25, 25, 25, 25, 139, 166, 166, 181, 181, 25, 25] 201 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 9, 35, 33, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 448 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113956 none NC(=O)N1CCC[C@H]1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 187, 201, 187, 187, 187, 187, 118, 187, 118, 118, 40, 40, 40, 11, 11, 11, 6, 2, 1, 1, 1, 1, 1, 1, 11, 11, 40, 201, 201, 187, 187, 187, 187, 187, 187, 118, 40, 40, 40, 40, 11, 6, 6, 2, 2, 40, 40] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 599 number of broken/clashed sets: 15 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113956 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113956/1 /scratch/stefan/7770410/working/building/REAL300020113956 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1528) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1528 `/scratch/stefan/7770410/working/3D/1528' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)N1CCC[C@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113956.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113956/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113956 none NC(=O)N1CCC[C@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 25, 51, 25, 25, 25, 25, 6, 25, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 27, 35, 35, 35, 35, 35, 13, 13, 1, 51, 51, 25, 25, 25, 25, 25, 25, 6, 1, 1, 1, 1, 13, 27, 27, 35, 35, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 274 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113956 none NC(=O)N1CCC[C@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [179, 140, 179, 140, 140, 140, 140, 61, 140, 61, 61, 13, 13, 13, 1, 1, 1, 1, 1, 7, 9, 9, 9, 9, 9, 1, 1, 13, 179, 179, 140, 140, 140, 140, 140, 140, 61, 13, 13, 13, 13, 1, 7, 7, 9, 9, 13, 13] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 580 number of broken/clashed sets: 15 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113956 none NC(=O)N1CCC[C@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 25, 25, 25, 140, 140, 140, 167, 181, 181, 181, 181, 181, 140, 140, 25, 5, 5, 1, 1, 1, 1, 1, 1, 8, 25, 25, 25, 25, 140, 167, 167, 181, 181, 25, 25] 201 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 9, 35, 33, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 443 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113956 none NC(=O)N1CCC[C@H]1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 186, 201, 186, 186, 186, 186, 126, 186, 126, 126, 43, 43, 43, 11, 11, 11, 6, 3, 1, 1, 1, 1, 1, 1, 11, 11, 43, 201, 201, 186, 186, 186, 186, 186, 186, 126, 43, 43, 43, 43, 11, 6, 6, 2, 2, 43, 43] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 599 number of broken/clashed sets: 15 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113956 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113956 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113956/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113956/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113956 Building REAL300020113957 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113957' /scratch/stefan/7770410/working/building/REAL300020113957 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113957 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113957/0 /scratch/stefan/7770410/working/building/REAL300020113957 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1529) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1529 `/scratch/stefan/7770410/working/3D/1529' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2=CN=CN2C1) `REAL300020113957.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113957 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2=CN=CN2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 8, 1, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 33, 106, 106, 106, 106, 106, 106, 106, 106, 33, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 106, 106, 106, 106, 106, 106, 106, 106, 106] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 307 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113957 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2=CN=CN2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 8, 1, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 54, 54, 54, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 54, 104, 201, 201, 201, 201, 201, 201, 201, 201, 104, 54, 54, 54, 54, 11, 6, 6, 4, 4, 54, 54, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 605 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113957 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2=CN=CN2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 8, 1, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 30, 46, 53, 53, 53, 53, 11, 11, 1, 6, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 30, 30, 46, 46, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113957 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2=CN=CN2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 8, 1, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 22, 22, 22, 106, 106, 106, 160, 201, 201, 201, 201, 201, 106, 106, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 22, 22, 22, 22, 106, 160, 160, 201, 201, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 702 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113957 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113957/1 /scratch/stefan/7770410/working/building/REAL300020113957 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1530) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1530 `/scratch/stefan/7770410/working/3D/1530' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2=CN=CN2C1) `REAL300020113957.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113957/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113957 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2=CN=CN2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 8, 1, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 33, 106, 106, 106, 106, 106, 106, 106, 106, 33, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 106, 106, 106, 106, 106, 106, 106, 106, 106] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 307 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113957 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2=CN=CN2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 8, 1, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 53, 53, 53, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 53, 104, 201, 201, 201, 201, 201, 201, 201, 201, 104, 53, 53, 53, 53, 10, 6, 6, 4, 4, 53, 53, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 607 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113957 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2=CN=CN2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 8, 1, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 30, 46, 53, 53, 53, 53, 11, 11, 1, 6, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 30, 30, 46, 46, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113957 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2=CN=CN2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 8, 1, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 22, 22, 22, 106, 106, 106, 160, 201, 201, 201, 201, 201, 106, 106, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 22, 22, 22, 22, 106, 160, 160, 201, 201, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 702 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113957 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113957 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113957/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113957/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113957 Building REAL300020113958 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113958' /scratch/stefan/7770410/working/building/REAL300020113958 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113958 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113958/0 /scratch/stefan/7770410/working/building/REAL300020113958 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1531) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1531 `/scratch/stefan/7770410/working/3D/1531' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CC=C21) `REAL300020113958.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113958 none CN1C=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 37, 52, 59, 59, 59, 59, 11, 11, 1, 16, 16, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 11, 37, 37, 52, 52, 1, 1, 16, 16] 201 rigid atoms, others: [45, 35, 36, 37, 38, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47]) total number of confs: 243 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113958 none CN1C=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 79, 79, 79, 30, 30, 30, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 1, 1, 11, 79, 79, 79, 79, 79, 79, 79, 79, 30, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 79, 79] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 191 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113958 none CN1C=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 79, 79, 79, 155, 201, 201, 201, 201, 201, 79, 79, 16, 1, 1, 1, 2, 2, 2, 1, 1, 5, 16, 16, 16, 16, 79, 155, 155, 201, 201, 16, 16, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 46, 47, 33, 27, 28, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 794 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113958 none CN1C=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 90, 90, 90, 59, 59, 59, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 59, 201, 201, 201, 201, 201, 201, 201, 201, 90, 59, 59, 59, 59, 14, 6, 6, 4, 4, 59, 59, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 427 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113958 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113958/1 /scratch/stefan/7770410/working/building/REAL300020113958 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1532) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1532 `/scratch/stefan/7770410/working/3D/1532' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CC=C21) `REAL300020113958.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113958 none CN1C=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 37, 52, 59, 59, 59, 59, 11, 11, 1, 16, 16, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 11, 37, 37, 52, 52, 1, 1, 16, 16] 201 rigid atoms, others: [45, 35, 36, 37, 38, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47]) total number of confs: 243 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113958 none CN1C=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 79, 79, 79, 30, 30, 30, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 1, 1, 11, 79, 79, 79, 79, 79, 79, 79, 79, 30, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 79, 79] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 191 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113958 none CN1C=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 79, 79, 79, 155, 201, 201, 201, 201, 201, 79, 79, 16, 1, 1, 1, 2, 2, 2, 1, 1, 5, 16, 16, 16, 16, 79, 155, 155, 201, 201, 16, 16, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 46, 47, 33, 27, 28, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 794 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113958 none CN1C=NC2=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 91, 91, 91, 59, 59, 59, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 59, 201, 201, 201, 201, 201, 201, 201, 201, 91, 59, 59, 59, 59, 13, 6, 6, 4, 4, 59, 59, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 429 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113958 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113958 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113958/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113958/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113958 Building REAL300020113959 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113959' /scratch/stefan/7770410/working/building/REAL300020113959 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113959 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113959/0 /scratch/stefan/7770410/working/building/REAL300020113959 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1533) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1533 `/scratch/stefan/7770410/working/3D/1533' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CCCC1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113959.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113959 none COC1CCCC1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 14, 14, 14, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 46, 61, 80, 80, 80, 80, 11, 11, 1, 23, 23, 23, 14, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 11, 46, 46, 61, 61, 1, 1] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 329 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113959 none COC1CCCC1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 76, 76, 76, 76, 76, 40, 40, 40, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 11, 90, 90, 90, 76, 76, 76, 76, 76, 76, 76, 76, 40, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 292 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113959 none COC1CCCC1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 76, 76, 76, 170, 201, 201, 201, 201, 201, 76, 76, 14, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 14, 14, 14, 14, 76, 170, 170, 201, 201, 14, 14] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 35, 36, 29, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 731 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113959 none COC1CCCC1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 157, 157, 157, 81, 81, 81, 16, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 81, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 157, 81, 81, 81, 81, 16, 6, 6, 4, 4, 81, 81] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 586 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113959 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113959/1 /scratch/stefan/7770410/working/building/REAL300020113959 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1534) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1534 `/scratch/stefan/7770410/working/3D/1534' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113959.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113959/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113959 none COC1CCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 14, 14, 14, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 45, 60, 79, 79, 79, 79, 11, 11, 1, 23, 23, 23, 14, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 11, 45, 45, 60, 60, 1, 1] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 326 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113959 none COC1CCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 77, 77, 77, 77, 77, 40, 40, 40, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 11, 91, 91, 91, 77, 77, 77, 77, 77, 77, 77, 77, 40, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 296 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113959 none COC1CCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 77, 77, 77, 170, 201, 201, 201, 201, 201, 77, 77, 14, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 14, 14, 14, 14, 77, 170, 170, 201, 201, 14, 14] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 35, 36, 29, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 729 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113959 none COC1CCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 155, 155, 155, 79, 79, 79, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 79, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 155, 79, 79, 79, 79, 15, 6, 6, 4, 4, 79, 79] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 591 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113959 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113959 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113959/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113959/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113959 Building REAL300020113960 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113960' /scratch/stefan/7770410/working/building/REAL300020113960 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113960 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113960/0 /scratch/stefan/7770410/working/building/REAL300020113960 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1535) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1535 `/scratch/stefan/7770410/working/3D/1535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CO1) `REAL300020113960.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113960 none CC1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 36, 54, 62, 62, 62, 62, 13, 13, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 1, 1, 1, 1, 13, 36, 36, 54, 54, 1, 1, 31, 31] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45]) total number of confs: 309 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113960 none CC1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [122, 122, 122, 58, 58, 58, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 13, 122, 122, 122, 122, 122, 122, 122, 122, 122, 58, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 122, 122] 201 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 368 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113960 none CC1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 8, 31, 31, 31, 122, 122, 122, 174, 201, 201, 201, 201, 201, 122, 122, 31, 1, 1, 2, 2, 2, 1, 1, 1, 1, 8, 31, 31, 31, 31, 122, 174, 174, 201, 201, 31, 31, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 44, 45, 23, 24, 28, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 628 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113960 none CC1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 148, 148, 148, 62, 62, 62, 9, 9, 9, 6, 4, 1, 1, 1, 1, 1, 1, 9, 9, 62, 201, 201, 201, 201, 201, 201, 201, 201, 201, 148, 62, 62, 62, 62, 9, 6, 6, 4, 4, 62, 62, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 590 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113960 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113960/1 /scratch/stefan/7770410/working/building/REAL300020113960 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1536) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1536 `/scratch/stefan/7770410/working/3D/1536' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CO1) `REAL300020113960.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113960/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113960 none CC1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 36, 54, 62, 62, 62, 62, 13, 13, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 1, 1, 1, 1, 13, 36, 36, 54, 54, 1, 1, 31, 31] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45]) total number of confs: 309 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113960 none CC1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [122, 122, 122, 58, 58, 58, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 13, 122, 122, 122, 122, 122, 122, 122, 122, 122, 58, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 122, 122] 201 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 368 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113960 none CC1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 8, 31, 31, 31, 122, 122, 122, 174, 201, 201, 201, 201, 201, 122, 122, 31, 1, 1, 2, 2, 2, 1, 1, 1, 1, 8, 31, 31, 31, 31, 122, 174, 174, 201, 201, 31, 31, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 44, 45, 23, 24, 28, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 628 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113960 none CC1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 149, 149, 149, 62, 62, 62, 9, 9, 9, 6, 4, 1, 1, 1, 1, 1, 1, 9, 9, 62, 201, 201, 201, 201, 201, 201, 201, 201, 201, 149, 62, 62, 62, 62, 9, 6, 6, 4, 4, 62, 62, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 588 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113960 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113960 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113960/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113960/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113960 Building REAL300020113961 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113961' /scratch/stefan/7770410/working/building/REAL300020113961 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113961 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113961/0 /scratch/stefan/7770410/working/building/REAL300020113961 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1537) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1537 `/scratch/stefan/7770410/working/3D/1537' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC2CC21) `REAL300020113961.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113961 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC2CC21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 54, 139, 139, 139, 139, 139, 139, 54, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 139, 139, 139, 139, 139, 139, 139, 139, 139, 139, 139] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 409 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113961 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC2CC21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 54, 54, 54, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 54, 131, 201, 201, 201, 201, 201, 201, 131, 54, 54, 54, 54, 8, 4, 4, 2, 2, 54, 54, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 595 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113961 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC2CC21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 38, 54, 54, 54, 54, 54, 13, 13, 1, 6, 36, 36, 36, 36, 36, 36, 6, 1, 1, 1, 1, 13, 38, 38, 54, 54, 1, 1, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 297 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113961 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCC2CC21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 36, 36, 36, 139, 139, 139, 182, 201, 201, 201, 201, 201, 139, 139, 36, 1, 1, 1, 1, 1, 1, 1, 12, 36, 36, 36, 36, 139, 182, 182, 201, 201, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 563 number of broken/clashed sets: 4 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113961 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113961/1 /scratch/stefan/7770410/working/building/REAL300020113961 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1538) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1538 `/scratch/stefan/7770410/working/3D/1538' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2CC21) `REAL300020113961.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113961 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2CC21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 54, 138, 138, 138, 138, 138, 138, 54, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 138, 138, 138, 138, 138, 138, 138, 138, 138, 138, 138] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 409 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113961 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2CC21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [132, 132, 54, 54, 54, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 54, 132, 201, 201, 201, 201, 201, 201, 132, 54, 54, 54, 54, 8, 4, 4, 2, 2, 54, 54, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 597 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113961 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2CC21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 38, 54, 54, 54, 54, 54, 13, 13, 1, 6, 36, 36, 36, 36, 36, 36, 6, 1, 1, 1, 1, 13, 38, 38, 54, 54, 1, 1, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 297 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113961 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCC2CC21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 36, 36, 36, 138, 138, 138, 181, 201, 201, 201, 201, 201, 138, 138, 36, 1, 1, 1, 1, 1, 1, 1, 12, 36, 36, 36, 36, 138, 181, 181, 201, 201, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 569 number of broken/clashed sets: 4 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113961 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113961 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113961/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113961/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113961 Building REAL300020113962 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113962' /scratch/stefan/7770410/working/building/REAL300020113962 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113962 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113962/0 /scratch/stefan/7770410/working/building/REAL300020113962 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1539) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1539 `/scratch/stefan/7770410/working/3D/1539' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCC2CC21)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113962.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113962 none O=C(CC1CCC2CC21)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 22, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 7, 7, 7, 23, 35, 35, 35, 35, 35, 7, 7, 1, 22, 22, 40, 40, 40, 40, 40, 40, 40, 40, 40, 5, 1, 1, 1, 1, 7, 23, 23, 35, 35, 1, 1] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 277 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113962 none O=C(CC1CCC2CC21)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 88, 121, 121, 121, 121, 121, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 88, 88, 121, 121, 121, 121, 121, 121, 121, 121, 121, 19, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 449 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113962 none O=C(CC1CCC2CC21)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 5, 1, 1, 1, 1, 1, 1, 1, 21, 21, 40, 40, 40, 121, 121, 121, 170, 201, 201, 201, 201, 201, 121, 121, 40, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 40, 40, 40, 40, 121, 170, 170, 201, 201, 40, 40] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 682 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113962 none O=C(CC1CCC2CC21)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 178, 201, 201, 201, 201, 201, 35, 35, 35, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 35, 178, 178, 201, 201, 201, 201, 201, 201, 201, 201, 201, 56, 35, 35, 35, 35, 8, 4, 4, 2, 2, 35, 35] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 749 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113962 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113962/1 /scratch/stefan/7770410/working/building/REAL300020113962 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1540) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1540 `/scratch/stefan/7770410/working/3D/1540' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCC2CC21)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113962.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113962/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113962 none O=C(CC1CCC2CC21)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 22, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 7, 7, 7, 23, 35, 35, 35, 35, 35, 7, 7, 1, 22, 22, 40, 40, 40, 40, 40, 40, 40, 40, 40, 5, 1, 1, 1, 1, 7, 23, 23, 35, 35, 1, 1] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 277 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113962 none O=C(CC1CCC2CC21)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 88, 121, 121, 121, 121, 121, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 88, 88, 121, 121, 121, 121, 121, 121, 121, 121, 121, 19, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 449 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113962 none O=C(CC1CCC2CC21)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 5, 1, 1, 1, 1, 1, 1, 1, 21, 21, 40, 40, 40, 121, 121, 121, 170, 201, 201, 201, 201, 201, 121, 121, 40, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 40, 40, 40, 40, 121, 170, 170, 201, 201, 40, 40] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 682 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113962 none O=C(CC1CCC2CC21)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 178, 201, 201, 201, 201, 201, 35, 35, 35, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 35, 178, 178, 201, 201, 201, 201, 201, 201, 201, 201, 201, 56, 35, 35, 35, 35, 8, 4, 4, 2, 2, 35, 35] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 749 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113962 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113962 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113962/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113962/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113962 Building REAL300020113963 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113963' /scratch/stefan/7770410/working/building/REAL300020113963 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113963 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113963/0 /scratch/stefan/7770410/working/building/REAL300020113963 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1541) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1541 `/scratch/stefan/7770410/working/3D/1541' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2CC2C1) `REAL300020113963.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113963 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2CC2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 50, 139, 139, 139, 139, 139, 139, 50, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 139, 139, 139, 139, 139, 139, 139, 139, 139, 139, 139] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 419 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113963 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2CC2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 40, 40, 40, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 40, 99, 201, 201, 201, 201, 201, 201, 99, 40, 40, 40, 40, 9, 4, 4, 2, 2, 40, 40, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 601 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113963 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2CC2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 29, 39, 39, 39, 39, 39, 13, 13, 1, 6, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 13, 29, 29, 39, 39, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 211 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113963 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC2CC2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 26, 26, 26, 139, 139, 139, 181, 201, 201, 201, 201, 201, 139, 139, 26, 1, 1, 1, 1, 1, 1, 1, 8, 26, 26, 26, 26, 139, 181, 181, 201, 201, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 552 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113963 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113963/1 /scratch/stefan/7770410/working/building/REAL300020113963 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1542) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1542 `/scratch/stefan/7770410/working/3D/1542' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2CC2C1) `REAL300020113963.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113963 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2CC2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 50, 139, 139, 139, 139, 139, 139, 50, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 139, 139, 139, 139, 139, 139, 139, 139, 139, 139, 139] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 419 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113963 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2CC2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 40, 40, 40, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 40, 99, 201, 201, 201, 201, 201, 201, 99, 40, 40, 40, 40, 9, 4, 4, 2, 2, 40, 40, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 601 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113963 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2CC2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 29, 39, 39, 39, 39, 39, 13, 13, 1, 6, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 13, 29, 29, 39, 39, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 211 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113963 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC2CC2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 26, 26, 26, 139, 139, 139, 181, 201, 201, 201, 201, 201, 139, 139, 26, 1, 1, 1, 1, 1, 1, 1, 8, 26, 26, 26, 26, 139, 181, 181, 201, 201, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 552 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113963 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113963 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113963/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113963/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113963 Building REAL300020113964 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113964' /scratch/stefan/7770410/working/building/REAL300020113964 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113964 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113964/0 /scratch/stefan/7770410/working/building/REAL300020113964 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1543) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1543 `/scratch/stefan/7770410/working/3D/1543' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(OC)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113964.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113964 none CCC(C)C(OC)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 100, 54, 100, 35, 54, 54, 35, 35, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 12, 12, 12, 12, 1, 1, 11, 103, 103, 103, 103, 103, 100, 100, 100, 100, 54, 54, 54, 54, 35, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [12, 44, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 456 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113964 none CCC(C)C(OC)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 139, 201, 85, 139, 139, 85, 85, 38, 38, 38, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 38, 201, 201, 201, 201, 201, 201, 201, 201, 201, 139, 139, 139, 139, 85, 38, 38, 38, 38, 8, 4, 4, 2, 2, 38, 38] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 837 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113964 none CCC(C)C(OC)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 25, 11, 25, 6, 11, 12, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 45, 54, 54, 54, 54, 11, 11, 1, 29, 29, 29, 29, 29, 25, 25, 25, 25, 11, 12, 12, 12, 6, 1, 1, 1, 1, 11, 31, 31, 45, 45, 1, 1] 201 rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 49, 50, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 326 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113964 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113964/1 /scratch/stefan/7770410/working/building/REAL300020113964 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1544) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1544 `/scratch/stefan/7770410/working/3D/1544' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(OC)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113964.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113964 none CCC(C)C(OC)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 101, 54, 101, 35, 54, 54, 35, 35, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 12, 12, 12, 12, 1, 1, 11, 104, 104, 104, 104, 104, 101, 101, 101, 101, 54, 54, 54, 54, 35, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [12, 44, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 462 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113964 none CCC(C)C(OC)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 140, 201, 85, 140, 140, 85, 85, 38, 38, 38, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 38, 201, 201, 201, 201, 201, 201, 201, 201, 201, 140, 140, 140, 140, 85, 38, 38, 38, 38, 8, 4, 4, 2, 2, 38, 38] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 837 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113964 none CCC(C)C(OC)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 25, 11, 25, 6, 11, 12, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 30, 44, 53, 53, 53, 53, 11, 11, 1, 29, 29, 29, 29, 29, 25, 25, 25, 25, 11, 12, 12, 12, 6, 1, 1, 1, 1, 11, 30, 30, 44, 44, 1, 1] 201 rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 49, 50, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 320 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113964 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113964 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113964/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113964/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113964 Building REAL300020113965 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113965' /scratch/stefan/7770410/working/building/REAL300020113965 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113965 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113965/0 /scratch/stefan/7770410/working/building/REAL300020113965 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1545) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1545 `/scratch/stefan/7770410/working/3D/1545' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1) `REAL300020113965.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113965 none COC1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 21, 21, 21, 21, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 31, 46, 52, 52, 52, 52, 11, 11, 1, 21, 33, 33, 33, 21, 21, 21, 21, 21, 21, 5, 1, 1, 1, 1, 11, 31, 31, 46, 46, 1, 1, 21, 21] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 45, 46, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 265 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113965 none COC1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 89, 89, 89, 89, 26, 26, 26, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 89, 113, 113, 113, 89, 89, 89, 89, 89, 89, 26, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 89, 89] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 303 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113965 none COC1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 9, 9, 9, 21, 21, 21, 89, 89, 89, 150, 196, 201, 201, 201, 201, 89, 89, 21, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 9, 21, 21, 21, 21, 89, 150, 150, 196, 196, 21, 21, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 34, 47, 48, 25, 29, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 726 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113965 none COC1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 90, 90, 90, 52, 52, 52, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 52, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 90, 52, 52, 52, 52, 11, 6, 6, 4, 4, 52, 52, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 579 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113965 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113965/1 /scratch/stefan/7770410/working/building/REAL300020113965 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1546) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1546 `/scratch/stefan/7770410/working/3D/1546' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1) `REAL300020113965.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113965 none COC1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 21, 21, 21, 21, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 31, 46, 52, 52, 52, 52, 11, 11, 1, 21, 33, 33, 33, 21, 21, 21, 21, 21, 21, 5, 1, 1, 1, 1, 11, 31, 31, 46, 46, 1, 1, 21, 21] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 45, 46, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 265 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113965 none COC1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 89, 89, 89, 89, 25, 25, 25, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 89, 113, 113, 113, 89, 89, 89, 89, 89, 89, 25, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 89, 89] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 303 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113965 none COC1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 9, 9, 9, 21, 21, 21, 89, 89, 89, 150, 196, 201, 201, 201, 201, 89, 89, 21, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 9, 21, 21, 21, 21, 89, 150, 150, 196, 196, 21, 21, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 34, 47, 48, 25, 29, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 725 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113965 none COC1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 89, 89, 89, 52, 52, 52, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 52, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 89, 52, 52, 52, 52, 11, 6, 6, 4, 4, 52, 52, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 579 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113965 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113965 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113965/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113965/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113965 Building REAL300020113966 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113966' /scratch/stefan/7770410/working/building/REAL300020113966 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113966 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113966/0 /scratch/stefan/7770410/working/building/REAL300020113966 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1547) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1547 `/scratch/stefan/7770410/working/3D/1547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1=O) `REAL300020113966.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113966 none CN1CCN(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 24, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 47, 56, 56, 56, 56, 11, 11, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 24, 24, 6, 1, 1, 1, 1, 11, 33, 33, 47, 47, 1, 1, 29, 29] 201 rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 47, 48, 40, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50]) total number of confs: 295 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113966 none CN1CCN(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 113, 101, 41, 41, 41, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 11, 113, 113, 113, 113, 113, 113, 113, 113, 113, 113, 101, 101, 41, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 113, 113] 201 rigid atoms, others: [42, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 419 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113966 none CN1CCN(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 29, 29, 29, 113, 113, 113, 171, 201, 201, 201, 201, 201, 113, 113, 29, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 5, 5, 11, 29, 29, 29, 29, 113, 171, 171, 201, 201, 29, 29, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 49, 50, 25, 26, 27, 5, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 671 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113966 none CN1CCN(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 126, 126, 126, 56, 56, 56, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 56, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 126, 56, 56, 56, 56, 13, 6, 6, 4, 4, 56, 56, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 724 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113966 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113966/1 /scratch/stefan/7770410/working/building/REAL300020113966 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1548) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1548 `/scratch/stefan/7770410/working/3D/1548' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1=O) `REAL300020113966.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113966 none CN1CCN(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 23, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 34, 48, 57, 57, 57, 57, 12, 12, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 23, 23, 6, 1, 1, 1, 1, 12, 34, 34, 48, 48, 1, 1, 28, 28] 201 rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 47, 48, 40, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50]) total number of confs: 293 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113966 none CN1CCN(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 112, 101, 41, 41, 41, 12, 12, 12, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 12, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 101, 101, 41, 12, 12, 12, 12, 1, 8, 8, 10, 10, 12, 12, 112, 112] 201 rigid atoms, others: [42, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 418 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113966 none CN1CCN(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 28, 28, 28, 112, 112, 112, 171, 201, 201, 201, 201, 201, 112, 112, 28, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 5, 5, 11, 28, 28, 28, 28, 112, 171, 171, 201, 201, 28, 28, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 49, 50, 25, 26, 27, 5, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 681 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113966 none CN1CCN(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 127, 127, 127, 56, 56, 56, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 56, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 127, 56, 56, 56, 56, 13, 6, 6, 4, 4, 56, 56, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 720 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113966 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113966 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113966/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113966/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113966 Building REAL300020113967 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113967' /scratch/stefan/7770410/working/building/REAL300020113967 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113967 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113967/0 /scratch/stefan/7770410/working/building/REAL300020113967 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1549) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1549 `/scratch/stefan/7770410/working/3D/1549' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=[NH+]C=C1) `REAL300020113967.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113967 none CN(CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=[NH+]C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 6, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 2 rigid atoms, others: [9, 42, 11, 12, 13, 20, 21, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 11 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113967 none CN(CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=[NH+]C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 6, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 1, 1, 4, 4, 4, 4, 4, 4] 4 rigid atoms, others: [45, 46, 13, 16, 17, 18, 19, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52]) total number of confs: 14 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113967 none CN(CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=[NH+]C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 6, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 2, 2, 2, 2] 2 rigid atoms, others: [6, 38, 7, 8, 9, 10, 39, 47, 48, 40, 22, 41] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50, 51, 52]) total number of confs: 7 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113967 none CN(CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=[NH+]C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 6, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1] 2 rigid atoms, others: [1, 49, 50, 51, 52, 23, 24, 25, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 5 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113967 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113967/1 /scratch/stefan/7770410/working/building/REAL300020113967 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1550) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1550 `/scratch/stefan/7770410/working/3D/1550' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=[NH+]C=C1) `REAL300020113967.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113967/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113967 none CN(CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=[NH+]C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 6, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 2 rigid atoms, others: [9, 42, 11, 12, 13, 20, 21, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 11 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113967 none CN(CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=[NH+]C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 6, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 1, 1, 4, 4, 4, 4, 4, 4] 4 rigid atoms, others: [45, 46, 13, 16, 17, 18, 19, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52]) total number of confs: 14 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113967 none CN(CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=[NH+]C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 6, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 2, 2, 2, 2] 2 rigid atoms, others: [6, 38, 7, 8, 9, 10, 39, 47, 48, 40, 22, 41] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50, 51, 52]) total number of confs: 7 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113967 none CN(CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=[NH+]C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 6, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1] 2 rigid atoms, others: [1, 49, 50, 51, 52, 23, 24, 25, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 5 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113967 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113967 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113967/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113967/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113967 Building REAL300020113968 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113968' /scratch/stefan/7770410/working/building/REAL300020113968 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113968 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113968/0 /scratch/stefan/7770410/working/building/REAL300020113968 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1551) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1551 `/scratch/stefan/7770410/working/3D/1551' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1C=C(C2CC2)C=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113968.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113968 none O=C(CN1C=C(C2CC2)C=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 5, 5, 5, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 9, 4, 4, 4, 1, 1, 1, 1, 4, 4, 17, 17, 33, 33, 33, 109, 109, 109, 173, 201, 201, 201, 201, 201, 109, 109, 33, 9, 9, 4, 1, 1, 1, 1, 1, 4, 17, 33, 33, 33, 33, 109, 173, 173, 201, 201, 33, 33] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 31] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 695 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113968 none O=C(CN1C=C(C2CC2)C=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 5, 5, 5, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 115, 116, 116, 116, 201, 201, 116, 116, 31, 31, 31, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 31, 115, 115, 116, 201, 201, 201, 201, 201, 116, 55, 31, 31, 31, 31, 8, 4, 4, 2, 2, 31, 31] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 771 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113968 none O=C(CN1C=C(C2CC2)C=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 5, 5, 5, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 15, 17, 17, 17, 33, 33, 17, 17, 1, 1, 1, 1, 1, 7, 7, 7, 19, 30, 30, 30, 30, 30, 7, 7, 1, 15, 15, 17, 33, 33, 33, 33, 33, 17, 5, 1, 1, 1, 1, 7, 19, 19, 30, 30, 1, 1] 201 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 244 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113968 none O=C(CN1C=C(C2CC2)C=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 5, 5, 5, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 4, 4, 1, 1, 9, 9, 17, 17, 17, 60, 60, 60, 97, 117, 117, 117, 117, 117, 60, 60, 17, 5, 5, 1, 4, 4, 4, 4, 4, 1, 9, 17, 17, 17, 17, 60, 97, 97, 117, 117, 17, 17] 201 rigid atoms, others: [2, 3, 4, 5, 6, 9, 10, 36, 30] set([0, 1, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 418 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113968 none O=C(CN1C=C(C2CC2)C=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 5, 5, 5, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 58, 60, 60, 60, 109, 109, 60, 60, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 58, 58, 60, 109, 109, 109, 109, 109, 60, 21, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 431 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113968 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113968/1 /scratch/stefan/7770410/working/building/REAL300020113968 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1552) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1552 `/scratch/stefan/7770410/working/3D/1552' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1C=C(C2CC2)C=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113968.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113968/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113968 none O=C(CN1C=C(C2CC2)C=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 5, 5, 5, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 9, 4, 4, 4, 1, 1, 1, 1, 4, 4, 17, 17, 33, 33, 33, 109, 109, 109, 173, 201, 201, 201, 201, 201, 109, 109, 33, 9, 9, 4, 1, 1, 1, 1, 1, 4, 17, 33, 33, 33, 33, 109, 173, 173, 201, 201, 33, 33] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 31] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 695 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113968 none O=C(CN1C=C(C2CC2)C=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 5, 5, 5, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 115, 116, 116, 116, 201, 201, 116, 116, 31, 31, 31, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 31, 115, 115, 116, 201, 201, 201, 201, 201, 116, 55, 31, 31, 31, 31, 8, 4, 4, 2, 2, 31, 31] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 771 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113968 none O=C(CN1C=C(C2CC2)C=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 5, 5, 5, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 15, 17, 17, 17, 33, 33, 17, 17, 1, 1, 1, 1, 1, 7, 7, 7, 19, 30, 30, 30, 30, 30, 7, 7, 1, 15, 15, 17, 33, 33, 33, 33, 33, 17, 5, 1, 1, 1, 1, 7, 19, 19, 30, 30, 1, 1] 201 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 244 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113968 none O=C(CN1C=C(C2CC2)C=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 5, 5, 5, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 4, 4, 1, 1, 9, 9, 17, 17, 17, 60, 60, 60, 96, 116, 116, 116, 116, 116, 60, 60, 17, 5, 5, 1, 4, 4, 4, 4, 4, 1, 9, 17, 17, 17, 17, 60, 96, 96, 116, 116, 17, 17] 201 rigid atoms, others: [2, 3, 4, 5, 6, 9, 10, 36, 30] set([0, 1, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 415 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113968 none O=C(CN1C=C(C2CC2)C=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 5, 5, 5, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 58, 60, 60, 60, 109, 109, 60, 60, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 58, 58, 60, 109, 109, 109, 109, 109, 60, 21, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 431 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113968 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113968 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113968/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113968/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113968 Building REAL300020113969 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113969' /scratch/stefan/7770410/working/building/REAL300020113969 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113969 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113969/0 /scratch/stefan/7770410/working/building/REAL300020113969 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1553) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1553 `/scratch/stefan/7770410/working/3D/1553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1CCCC1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113969.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113969 none CCCC1CCCC1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 20, 20, 20, 20, 20, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 25, 38, 38, 38, 38, 38, 8, 8, 1, 30, 30, 30, 30, 30, 30, 30, 20, 20, 20, 20, 20, 20, 20, 20, 5, 1, 1, 1, 1, 8, 25, 25, 38, 38, 1, 1] 201 rigid atoms, others: [11, 44, 10, 43, 12, 13, 14, 45, 52, 46, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 264 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113969 none CCCC1CCCC1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 72, 72, 72, 72, 72, 22, 22, 22, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 109, 109, 109, 109, 109, 109, 109, 72, 72, 72, 72, 72, 72, 72, 72, 22, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [13, 14, 47, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 439 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113969 none CCCC1CCCC1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 20, 20, 20, 72, 72, 72, 120, 156, 156, 156, 156, 156, 72, 72, 20, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 20, 20, 20, 20, 72, 120, 120, 156, 156, 20, 20] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 40, 41, 39, 34, 8, 35, 36, 38, 37] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 583 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113969 none CCCC1CCCC1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 156, 156, 156, 156, 156, 64, 64, 64, 38, 38, 38, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 38, 201, 201, 201, 201, 201, 201, 201, 156, 156, 156, 156, 156, 156, 156, 156, 64, 38, 38, 38, 38, 8, 4, 4, 2, 2, 38, 38] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 717 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113969 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113969/1 /scratch/stefan/7770410/working/building/REAL300020113969 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1554) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1554 `/scratch/stefan/7770410/working/3D/1554' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1CCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113969.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113969/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113969 none CCCC1CCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 20, 20, 20, 20, 20, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 25, 38, 38, 38, 38, 38, 8, 8, 1, 30, 30, 30, 30, 30, 30, 30, 20, 20, 20, 20, 20, 20, 20, 20, 5, 1, 1, 1, 1, 8, 25, 25, 38, 38, 1, 1] 201 rigid atoms, others: [11, 44, 10, 43, 12, 13, 14, 45, 52, 46, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 264 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113969 none CCCC1CCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 73, 73, 73, 73, 73, 22, 22, 22, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 110, 110, 110, 110, 110, 110, 110, 73, 73, 73, 73, 73, 73, 73, 73, 22, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [13, 14, 47, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 443 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113969 none CCCC1CCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 20, 20, 20, 73, 73, 73, 121, 156, 156, 156, 156, 156, 73, 73, 20, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 20, 20, 20, 20, 73, 121, 121, 156, 156, 20, 20] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 40, 41, 39, 34, 8, 35, 36, 38, 37] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 579 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113969 none CCCC1CCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 156, 156, 156, 156, 156, 65, 65, 65, 38, 38, 38, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 38, 201, 201, 201, 201, 201, 201, 201, 156, 156, 156, 156, 156, 156, 156, 156, 65, 38, 38, 38, 38, 8, 4, 4, 2, 2, 38, 38] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 717 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113969 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113969 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113969/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113969/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113969 Building REAL300020113970 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113970' /scratch/stefan/7770410/working/building/REAL300020113970 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113970 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113970/0 /scratch/stefan/7770410/working/building/REAL300020113970 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1555) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1555 `/scratch/stefan/7770410/working/3D/1555' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C12CC3CC(C(=O)N1)C2C3) `REAL300020113970.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113970 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C12CC3CC(C(=O)N1)C2C3 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 35, 105, 105, 105, 105, 105, 105, 105, 105, 105, 35, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 105, 105, 105, 105, 105, 105, 105, 105, 105, 105] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 221 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113970 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C12CC3CC(C(=O)N1)C2C3 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 57, 57, 57, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 57, 115, 201, 201, 201, 201, 201, 201, 201, 201, 201, 115, 57, 57, 57, 57, 12, 6, 6, 4, 4, 57, 57, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 467 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113970 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C12CC3CC(C(=O)N1)C2C3 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 34, 48, 55, 55, 55, 55, 11, 11, 1, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 1, 1, 1, 1, 11, 34, 34, 48, 48, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113970 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C12CC3CC(C(=O)N1)C2C3 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 25, 25, 25, 105, 105, 105, 167, 201, 201, 201, 201, 201, 105, 105, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 25, 25, 25, 25, 105, 167, 167, 201, 201, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 702 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113970 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113970/1 /scratch/stefan/7770410/working/building/REAL300020113970 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1556) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1556 `/scratch/stefan/7770410/working/3D/1556' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C12CC3CC(C(=O)N1)C2C3) `REAL300020113970.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113970/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113970 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C12CC3CC(C(=O)N1)C2C3 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 34, 105, 105, 105, 105, 105, 105, 105, 105, 105, 34, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 105, 105, 105, 105, 105, 105, 105, 105, 105, 105] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 220 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113970 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C12CC3CC(C(=O)N1)C2C3 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 57, 57, 57, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 57, 115, 201, 201, 201, 201, 201, 201, 201, 201, 201, 115, 57, 57, 57, 57, 13, 6, 6, 4, 4, 57, 57, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 466 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113970 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C12CC3CC(C(=O)N1)C2C3 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 35, 49, 56, 56, 56, 56, 11, 11, 1, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 1, 1, 1, 1, 11, 35, 35, 49, 49, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113970 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C12CC3CC(C(=O)N1)C2C3 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 25, 25, 25, 105, 105, 105, 166, 201, 201, 201, 201, 201, 105, 105, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 25, 25, 25, 25, 105, 166, 166, 201, 201, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 710 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113970 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113970 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113970/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113970/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113970 Building REAL300020113971 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113971' /scratch/stefan/7770410/working/building/REAL300020113971 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113971 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113971/0 /scratch/stefan/7770410/working/building/REAL300020113971 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1557) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1557 `/scratch/stefan/7770410/working/3D/1557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)C(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113971.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113971 none CCC(CC)C(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 63, 61, 65, 92, 19, 61, 19, 19, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 8, 8, 8, 8, 1, 1, 8, 92, 92, 92, 92, 90, 65, 92, 92, 92, 92, 92, 61, 61, 61, 61, 19, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [12, 13, 46, 15, 16, 14, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 604 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113971 none CCC(CC)C(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 139, 139, 139, 201, 56, 139, 56, 56, 36, 36, 36, 8, 8, 8, 5, 3, 1, 1, 1, 1, 1, 1, 8, 8, 36, 201, 201, 201, 201, 201, 139, 201, 201, 201, 201, 201, 139, 139, 139, 139, 56, 36, 36, 36, 36, 8, 5, 5, 3, 3, 36, 36] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 1257 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113971 none CCC(CC)C(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 18, 16, 19, 25, 6, 16, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 36, 36, 36, 36, 8, 8, 1, 25, 25, 25, 25, 24, 19, 25, 25, 25, 25, 25, 16, 16, 16, 16, 6, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1] 201 rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 44, 51, 52, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50]) total number of confs: 288 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113971 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113971/1 /scratch/stefan/7770410/working/building/REAL300020113971 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1558) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1558 `/scratch/stefan/7770410/working/3D/1558' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)C(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113971.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113971 none CCC(CC)C(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 65, 63, 67, 94, 19, 63, 19, 19, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 8, 8, 8, 8, 1, 1, 8, 94, 94, 94, 94, 92, 67, 94, 94, 94, 94, 94, 63, 63, 63, 63, 19, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [12, 13, 46, 15, 16, 14, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 610 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113971 none CCC(CC)C(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 139, 139, 139, 201, 56, 139, 56, 56, 36, 36, 36, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 36, 201, 201, 201, 201, 201, 139, 201, 201, 201, 201, 201, 139, 139, 139, 139, 56, 36, 36, 36, 36, 9, 5, 5, 3, 3, 36, 36] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 1257 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113971 none CCC(CC)C(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 18, 16, 19, 25, 6, 16, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 21, 33, 34, 34, 34, 34, 8, 8, 1, 25, 25, 25, 25, 24, 19, 25, 25, 25, 25, 25, 16, 16, 16, 16, 6, 1, 1, 1, 1, 8, 21, 21, 33, 33, 1, 1] 201 rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 44, 51, 52, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50]) total number of confs: 282 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113971 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113971 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113971/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113971/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113971 Building REAL300020113972 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113972' /scratch/stefan/7770410/working/building/REAL300020113972 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113972 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113972/0 /scratch/stefan/7770410/working/building/REAL300020113972 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1559) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1559 `/scratch/stefan/7770410/working/3D/1559' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CS(=O)(=O)C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113972.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113972 none O=C(CC1CS(=O)(=O)C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 14, 11, 11, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 22, 44, 44, 44, 44, 44, 1, 1, 1, 1, 1, 11, 11, 11, 27, 39, 39, 39, 39, 39, 11, 11, 1, 22, 22, 44, 44, 44, 44, 44, 5, 1, 1, 1, 1, 11, 27, 27, 39, 39, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 303 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113972 none O=C(CC1CS(=O)(=O)C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 14, 11, 11, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 88, 129, 129, 129, 129, 129, 11, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 11, 88, 88, 129, 129, 129, 129, 129, 25, 11, 11, 11, 11, 1, 5, 5, 7, 7, 11, 11] 201 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 503 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113972 none O=C(CC1CS(=O)(=O)C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 14, 11, 11, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 5, 1, 1, 1, 1, 1, 1, 1, 22, 22, 44, 44, 44, 129, 129, 129, 163, 201, 201, 201, 201, 201, 129, 129, 44, 5, 5, 1, 1, 1, 1, 1, 22, 44, 44, 44, 44, 129, 163, 163, 201, 201, 44, 44] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 664 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113972 none O=C(CC1CS(=O)(=O)C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 14, 11, 11, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 158, 201, 201, 201, 201, 201, 39, 39, 39, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 39, 158, 158, 201, 201, 201, 201, 201, 69, 39, 39, 39, 39, 8, 4, 4, 2, 2, 39, 39] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 784 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113972 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113972/1 /scratch/stefan/7770410/working/building/REAL300020113972 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1560) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1560 `/scratch/stefan/7770410/working/3D/1560' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CS(=O)(=O)C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113972.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113972 none O=C(CC1CS(=O)(=O)C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 14, 11, 11, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 22, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 11, 11, 11, 27, 39, 39, 39, 39, 39, 11, 11, 1, 22, 22, 45, 45, 45, 45, 45, 5, 1, 1, 1, 1, 11, 27, 27, 39, 39, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 307 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113972 none O=C(CC1CS(=O)(=O)C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 14, 11, 11, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 87, 129, 129, 129, 129, 129, 11, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 11, 87, 87, 129, 129, 129, 129, 129, 25, 11, 11, 11, 11, 1, 5, 5, 7, 7, 11, 11] 201 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 504 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113972 none O=C(CC1CS(=O)(=O)C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 14, 11, 11, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 5, 1, 1, 1, 1, 1, 1, 1, 22, 22, 45, 45, 45, 129, 129, 129, 163, 201, 201, 201, 201, 201, 129, 129, 45, 5, 5, 1, 1, 1, 1, 1, 22, 45, 45, 45, 45, 129, 163, 163, 201, 201, 45, 45] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 664 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113972 none O=C(CC1CS(=O)(=O)C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 14, 11, 11, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 158, 201, 201, 201, 201, 201, 39, 39, 39, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 39, 158, 158, 201, 201, 201, 201, 201, 69, 39, 39, 39, 39, 8, 4, 4, 2, 2, 39, 39] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 784 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113972 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113972 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113972/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113972/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113972 Building REAL300020113973 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113973' /scratch/stefan/7770410/working/building/REAL300020113973 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113973 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113973/0 /scratch/stefan/7770410/working/building/REAL300020113973 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1561) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1561 `/scratch/stefan/7770410/working/3D/1561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C(F)(F)F)OC=N1) `REAL300020113973.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113973 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C(F)(F)F)OC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 15, 12, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 59, 106, 106, 106, 106, 106, 106, 106, 106, 59, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 106] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 259 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113973 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C(F)(F)F)OC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 15, 12, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [138, 138, 51, 51, 51, 9, 9, 9, 5, 2, 1, 1, 1, 1, 1, 1, 9, 9, 51, 138, 201, 201, 201, 201, 201, 201, 201, 201, 138, 51, 51, 51, 51, 9, 5, 5, 2, 2, 51, 51, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 500 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113973 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C(F)(F)F)OC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 15, 12, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 36, 50, 50, 50, 50, 50, 13, 13, 1, 6, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 36, 36, 50, 50, 1, 1, 16] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113973 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C(F)(F)F)OC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 15, 12, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 16, 16, 16, 106, 106, 106, 167, 201, 201, 201, 201, 201, 106, 106, 16, 1, 1, 1, 2, 2, 2, 1, 1, 1, 7, 16, 16, 16, 16, 106, 167, 167, 201, 201, 16, 16, 1] 201 rigid atoms, others: [1, 40, 19, 20, 21, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 667 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113973 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113973/1 /scratch/stefan/7770410/working/building/REAL300020113973 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1562) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1562 `/scratch/stefan/7770410/working/3D/1562' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C(F)(F)F)OC=N1) `REAL300020113973.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113973/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113973 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C(F)(F)F)OC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 15, 12, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 59, 105, 105, 105, 105, 105, 105, 105, 105, 59, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 105] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 257 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113973 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C(F)(F)F)OC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 15, 12, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [138, 138, 53, 53, 53, 11, 11, 11, 5, 2, 1, 1, 1, 1, 1, 1, 11, 11, 53, 138, 201, 201, 201, 201, 201, 201, 201, 201, 138, 53, 53, 53, 53, 11, 5, 5, 2, 2, 53, 53, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 497 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113973 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C(F)(F)F)OC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 15, 12, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 36, 50, 50, 50, 50, 50, 13, 13, 1, 6, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 36, 36, 50, 50, 1, 1, 16] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113973 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C(F)(F)F)OC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 15, 12, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 16, 16, 16, 105, 105, 105, 166, 201, 201, 201, 201, 201, 105, 105, 16, 1, 1, 1, 2, 2, 2, 1, 1, 1, 7, 16, 16, 16, 16, 105, 166, 166, 201, 201, 16, 16, 1] 201 rigid atoms, others: [1, 40, 19, 20, 21, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 672 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113973 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113973 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113973/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113973/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113973 Building REAL300020113974 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113974' /scratch/stefan/7770410/working/building/REAL300020113974 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113974 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113974/0 /scratch/stefan/7770410/working/building/REAL300020113974 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1563) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1563 `/scratch/stefan/7770410/working/3D/1563' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=NN(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1=O) `REAL300020113974.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113974 none CN1C=NN(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 17, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 28, 41, 44, 44, 44, 44, 11, 11, 1, 32, 32, 32, 32, 32, 32, 17, 17, 6, 1, 1, 1, 1, 11, 28, 28, 41, 41, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 248 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113974 none CN1C=NN(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 114, 77, 30, 30, 30, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 114, 114, 114, 114, 114, 114, 77, 77, 30, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 384 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113974 none CN1C=NN(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 14, 14, 14, 32, 32, 32, 114, 114, 114, 175, 201, 201, 201, 201, 201, 114, 114, 32, 1, 1, 2, 2, 2, 1, 5, 5, 14, 32, 32, 32, 32, 114, 175, 175, 201, 201, 32, 32] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 26, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 678 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113974 none CN1C=NN(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 175, 97, 97, 97, 46, 46, 46, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 46, 201, 201, 201, 201, 201, 201, 175, 175, 97, 46, 46, 46, 46, 11, 6, 6, 4, 4, 46, 46] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 700 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113974 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113974/1 /scratch/stefan/7770410/working/building/REAL300020113974 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1564) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1564 `/scratch/stefan/7770410/working/3D/1564' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=NN(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1=O) `REAL300020113974.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113974 none CN1C=NN(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 17, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 27, 40, 43, 43, 43, 43, 11, 11, 1, 32, 32, 32, 32, 32, 32, 17, 17, 6, 1, 1, 1, 1, 11, 27, 27, 40, 40, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 242 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113974 none CN1C=NN(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 115, 115, 77, 30, 30, 30, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 115, 115, 115, 115, 115, 115, 77, 77, 30, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 385 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113974 none CN1C=NN(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 14, 14, 14, 32, 32, 32, 115, 115, 115, 175, 201, 201, 201, 201, 201, 115, 115, 32, 1, 1, 2, 2, 2, 1, 5, 5, 14, 32, 32, 32, 32, 115, 175, 175, 201, 201, 32, 32] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 26, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 673 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113974 none CN1C=NN(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 175, 96, 96, 96, 45, 45, 45, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 45, 201, 201, 201, 201, 201, 201, 175, 175, 96, 45, 45, 45, 45, 11, 6, 6, 4, 4, 45, 45] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 701 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113974 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113974 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113974/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113974/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113974 Building REAL300020113975 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113975' /scratch/stefan/7770410/working/building/REAL300020113975 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113975 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113975/0 /scratch/stefan/7770410/working/building/REAL300020113975 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1565) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1565 `/scratch/stefan/7770410/working/3D/1565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2C=CC=CN12) `REAL300020113975.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113975 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2C=CC=CN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 1, 1, 11, 39, 106, 106, 106, 106, 106, 106, 106, 106, 39, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 106, 106, 106, 106, 106] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 235 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113975 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2C=CC=CN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [160, 160, 81, 81, 81, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 81, 160, 201, 201, 201, 201, 201, 201, 201, 201, 160, 81, 81, 81, 81, 15, 6, 6, 4, 4, 81, 81, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 522 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113975 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2C=CC=CN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 47, 65, 80, 80, 80, 80, 11, 11, 1, 5, 21, 21, 21, 21, 21, 21, 21, 21, 5, 1, 1, 1, 1, 11, 47, 47, 65, 65, 1, 1, 21, 21, 21, 21, 21] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 318 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113975 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2C=CC=CN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 21, 21, 21, 106, 106, 106, 169, 201, 201, 201, 201, 201, 106, 106, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 21, 21, 21, 21, 106, 169, 169, 201, 201, 21, 21, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 680 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113975 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113975/1 /scratch/stefan/7770410/working/building/REAL300020113975 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1566) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1566 `/scratch/stefan/7770410/working/3D/1566' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2C=CC=CN12) `REAL300020113975.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113975 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2C=CC=CN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 1, 1, 11, 39, 106, 106, 106, 106, 106, 106, 106, 106, 39, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 106, 106, 106, 106, 106] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 235 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113975 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2C=CC=CN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 81, 81, 81, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 81, 158, 201, 201, 201, 201, 201, 201, 201, 201, 158, 81, 81, 81, 81, 15, 6, 6, 4, 4, 81, 81, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 521 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113975 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2C=CC=CN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 47, 65, 80, 80, 80, 80, 11, 11, 1, 5, 21, 21, 21, 21, 21, 21, 21, 21, 5, 1, 1, 1, 1, 11, 47, 47, 65, 65, 1, 1, 21, 21, 21, 21, 21] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 318 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113975 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2C=CC=CN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 21, 21, 21, 106, 106, 106, 169, 201, 201, 201, 201, 201, 106, 106, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 21, 21, 21, 21, 106, 169, 169, 201, 201, 21, 21, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 680 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113975 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113975 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113975/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113975/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113975 Building REAL300020113976 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113976' /scratch/stefan/7770410/working/building/REAL300020113976 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113976 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113976/0 /scratch/stefan/7770410/working/building/REAL300020113976 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1567) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1567 `/scratch/stefan/7770410/working/3D/1567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC2=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)N=CN2C=C1) `REAL300020113976.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113976 none CC1=CC2=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)N=CN2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 69, 90, 111, 111, 111, 111, 12, 12, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 12, 69, 69, 90, 90, 1, 1, 17, 17, 17] 201 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 413 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113976 none CC1=CC2=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)N=CN2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 88, 52, 52, 52, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 19, 19, 19, 19, 1, 1, 12, 88, 88, 88, 88, 88, 88, 88, 88, 88, 52, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 88, 88, 88] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 245 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113976 none CC1=CC2=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)N=CN2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 88, 88, 88, 160, 201, 201, 201, 201, 201, 88, 88, 17, 1, 1, 1, 1, 1, 2, 2, 2, 1, 5, 17, 17, 17, 17, 88, 160, 160, 201, 201, 17, 17, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 45, 46, 47, 24, 25, 26, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 735 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113976 none CC1=CC2=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)N=CN2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 194, 194, 194, 111, 111, 111, 21, 21, 21, 6, 4, 1, 1, 1, 1, 1, 1, 21, 21, 111, 201, 201, 201, 201, 201, 201, 201, 201, 201, 194, 111, 111, 111, 111, 21, 6, 6, 4, 4, 111, 111, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 537 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113976 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113976/1 /scratch/stefan/7770410/working/building/REAL300020113976 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1568) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1568 `/scratch/stefan/7770410/working/3D/1568' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC2=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)N=CN2C=C1) `REAL300020113976.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113976 none CC1=CC2=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)N=CN2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 69, 90, 111, 111, 111, 111, 12, 12, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 12, 69, 69, 90, 90, 1, 1, 17, 17, 17] 201 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 413 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113976 none CC1=CC2=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)N=CN2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 88, 52, 52, 52, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 19, 19, 19, 19, 1, 1, 12, 88, 88, 88, 88, 88, 88, 88, 88, 88, 52, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 88, 88, 88] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 245 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113976 none CC1=CC2=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)N=CN2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 88, 88, 88, 160, 201, 201, 201, 201, 201, 88, 88, 17, 1, 1, 1, 1, 1, 2, 2, 2, 1, 5, 17, 17, 17, 17, 88, 160, 160, 201, 201, 17, 17, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 45, 46, 47, 24, 25, 26, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 735 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113976 none CC1=CC2=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)N=CN2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 194, 194, 194, 111, 111, 111, 21, 21, 21, 6, 4, 1, 1, 1, 1, 1, 1, 21, 21, 111, 201, 201, 201, 201, 201, 201, 201, 201, 201, 194, 111, 111, 111, 111, 21, 6, 6, 4, 4, 111, 111, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 537 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113976 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113976 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113976/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113976/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113976 Building REAL300020113977 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113977' /scratch/stefan/7770410/working/building/REAL300020113977 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113977 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113977/0 /scratch/stefan/7770410/working/building/REAL300020113977 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1569) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1569 `/scratch/stefan/7770410/working/3D/1569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C2=CNN=C2C=C1) `REAL300020113977.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113977 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C2=CNN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 26, 36, 42, 42, 42, 42, 6, 6, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 6, 26, 26, 36, 36, 1, 1, 23, 23, 23, 23] 125 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 42, 43, 21] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 188 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113977 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C2=CNN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 9, 13, 16, 16, 16, 16, 1, 1, 6, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 22, 6, 6, 6, 6, 1, 9, 9, 13, 13, 6, 6, 62, 62, 62, 62] 125 rigid atoms, others: [37, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 169 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113977 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C2=CNN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 23, 23, 23, 62, 62, 62, 106, 125, 125, 125, 125, 125, 62, 62, 23, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 23, 23, 23, 23, 62, 106, 106, 125, 125, 23, 23, 1, 1, 1, 1] 125 rigid atoms, others: [0, 1, 2, 3, 44, 45, 46, 47, 22, 23, 24, 25, 26, 27, 28] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 458 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113977 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C2=CNN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 72, 72, 72, 45, 45, 45, 21, 21, 21, 7, 4, 1, 1, 1, 1, 1, 1, 21, 21, 45, 125, 125, 125, 125, 125, 125, 125, 125, 125, 125, 72, 45, 45, 45, 45, 21, 7, 7, 4, 4, 45, 45, 125, 125, 125, 125] 125 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 290 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113977 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113977/1 /scratch/stefan/7770410/working/building/REAL300020113977 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1570) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1570 `/scratch/stefan/7770410/working/3D/1570' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C2=CNN=C2C=C1) `REAL300020113977.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113977 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C2=CNN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 26, 36, 42, 42, 42, 42, 6, 6, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 6, 26, 26, 36, 36, 1, 1, 23, 23, 23, 23] 125 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 42, 43, 21] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 188 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113977 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C2=CNN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 9, 13, 16, 16, 16, 16, 1, 1, 6, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 22, 6, 6, 6, 6, 1, 9, 9, 13, 13, 6, 6, 62, 62, 62, 62] 125 rigid atoms, others: [37, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 169 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113977 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C2=CNN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 23, 23, 23, 62, 62, 62, 106, 125, 125, 125, 125, 125, 62, 62, 23, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 23, 23, 23, 23, 62, 106, 106, 125, 125, 23, 23, 1, 1, 1, 1] 125 rigid atoms, others: [0, 1, 2, 3, 44, 45, 46, 47, 22, 23, 24, 25, 26, 27, 28] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 458 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113977 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C2=CNN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 73, 73, 73, 46, 46, 46, 21, 21, 21, 7, 4, 1, 1, 1, 1, 1, 1, 21, 21, 46, 125, 125, 125, 125, 125, 125, 125, 125, 125, 125, 73, 46, 46, 46, 46, 21, 7, 7, 4, 4, 46, 46, 125, 125, 125, 125] 125 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 293 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113977 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113977 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113977/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113977/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113977 Building REAL300020113978 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113978' /scratch/stefan/7770410/working/building/REAL300020113978 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113978 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113978/0 /scratch/stefan/7770410/working/building/REAL300020113978 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1571) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1571 `/scratch/stefan/7770410/working/3D/1571' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2OC=CC2=CC(F)=C1) `REAL300020113978.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113978 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2OC=CC2=CC(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 8, 12, 15, 15, 15, 15, 1, 1, 6, 22, 94, 94, 94, 94, 94, 94, 94, 94, 94, 22, 6, 6, 6, 6, 1, 8, 8, 12, 12, 6, 6, 94, 94, 94, 94] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 201 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113978 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2OC=CC2=CC(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 47, 47, 47, 19, 19, 19, 7, 4, 1, 1, 1, 1, 1, 1, 19, 19, 47, 86, 201, 201, 201, 201, 201, 201, 201, 201, 201, 86, 47, 47, 47, 47, 19, 7, 7, 4, 4, 47, 47, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 414 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113978 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2OC=CC2=CC(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 27, 37, 42, 42, 42, 42, 6, 6, 1, 6, 46, 46, 46, 46, 46, 46, 45, 46, 46, 6, 1, 1, 1, 1, 6, 27, 27, 37, 37, 1, 1, 46, 46, 46, 46] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113978 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2OC=CC2=CC(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 46, 46, 46, 94, 94, 94, 171, 201, 201, 201, 201, 201, 94, 94, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 46, 46, 46, 46, 94, 171, 171, 201, 201, 46, 46, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 734 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113978 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113978/1 /scratch/stefan/7770410/working/building/REAL300020113978 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1572) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1572 `/scratch/stefan/7770410/working/3D/1572' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2OC=CC2=CC(F)=C1) `REAL300020113978.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113978 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2OC=CC2=CC(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 8, 12, 16, 16, 16, 16, 1, 1, 6, 22, 94, 94, 94, 94, 94, 94, 94, 94, 94, 22, 6, 6, 6, 6, 1, 8, 8, 12, 12, 6, 6, 94, 94, 94, 94] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 203 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113978 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2OC=CC2=CC(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 48, 48, 48, 20, 20, 20, 7, 4, 1, 1, 1, 1, 1, 1, 20, 20, 48, 88, 201, 201, 201, 201, 201, 201, 201, 201, 201, 88, 48, 48, 48, 48, 20, 7, 7, 4, 4, 48, 48, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 416 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113978 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2OC=CC2=CC(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 27, 37, 43, 43, 43, 43, 6, 6, 1, 6, 45, 45, 45, 45, 45, 45, 44, 45, 45, 6, 1, 1, 1, 1, 6, 27, 27, 37, 37, 1, 1, 45, 45, 45, 45] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113978 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2OC=CC2=CC(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 45, 45, 45, 94, 94, 94, 171, 201, 201, 201, 201, 201, 94, 94, 45, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 45, 45, 45, 45, 94, 171, 171, 201, 201, 45, 45, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 734 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113978 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113978 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113978/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113978/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113978 Building REAL300020113979 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113979' /scratch/stefan/7770410/working/building/REAL300020113979 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113979 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113979/0 /scratch/stefan/7770410/working/building/REAL300020113979 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1573) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1573 `/scratch/stefan/7770410/working/3D/1573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2NC(=O)NC2=C1) `REAL300020113979.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113979 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2NC(=O)NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 11, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 29, 76, 76, 76, 76, 76, 76, 76, 76, 76, 29, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 76, 76, 76, 76] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 175 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113979 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2NC(=O)NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 11, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 46, 46, 46, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 46, 82, 201, 201, 201, 201, 201, 201, 201, 201, 201, 82, 46, 46, 46, 46, 10, 6, 6, 4, 4, 46, 46, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 421 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113979 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2NC(=O)NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 11, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 28, 42, 46, 46, 46, 46, 9, 9, 1, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 9, 28, 28, 42, 42, 1, 1, 15, 15, 15, 15] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113979 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN=C2NC(=O)NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 11, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 15, 15, 15, 76, 76, 76, 149, 201, 201, 201, 201, 201, 76, 76, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 76, 149, 149, 201, 201, 15, 15, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 798 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113979 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113979/1 /scratch/stefan/7770410/working/building/REAL300020113979 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1574) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1574 `/scratch/stefan/7770410/working/3D/1574' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2NC(=O)NC2=C1) `REAL300020113979.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113979 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2NC(=O)NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 11, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 29, 76, 76, 76, 76, 76, 76, 76, 76, 76, 29, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 76, 76, 76, 76] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 175 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113979 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2NC(=O)NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 11, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 46, 46, 46, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 46, 83, 201, 201, 201, 201, 201, 201, 201, 201, 201, 83, 46, 46, 46, 46, 10, 6, 6, 4, 4, 46, 46, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 423 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113979 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2NC(=O)NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 11, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 28, 42, 46, 46, 46, 46, 9, 9, 1, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 9, 28, 28, 42, 42, 1, 1, 15, 15, 15, 15] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113979 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN=C2NC(=O)NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 8, 1, 11, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 15, 15, 15, 76, 76, 76, 149, 201, 201, 201, 201, 201, 76, 76, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 76, 149, 149, 201, 201, 15, 15, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 798 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113979 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113979 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113979/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113979/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113979 Building REAL300020113980 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113980' /scratch/stefan/7770410/working/building/REAL300020113980 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113980 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113980/0 /scratch/stefan/7770410/working/building/REAL300020113980 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1575) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1575 `/scratch/stefan/7770410/working/3D/1575' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CNC(C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113980.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113980 none CC(=O)NC1=CNC(C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 30, 30, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 45, 45, 45, 45, 45, 11, 11, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 6, 1, 1, 1, 1, 11, 31, 31, 45, 45, 1, 1] 201 rigid atoms, others: [48, 39, 40, 41, 42, 12, 13, 14, 15, 16, 49, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 221 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113980 none CC(=O)NC1=CNC(C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 106, 106, 106, 106, 106, 106, 33, 33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 106, 106, 106, 106, 106, 106, 106, 106, 106, 33, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [43, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 210 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113980 none CC(=O)NC1=CNC(C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 30, 30, 30, 106, 106, 106, 166, 201, 201, 201, 201, 201, 106, 106, 30, 2, 2, 2, 2, 1, 1, 2, 2, 2, 11, 30, 30, 30, 30, 106, 166, 166, 201, 201, 30, 30] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 712 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113980 none CC(=O)NC1=CNC(C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 97, 97, 97, 46, 46, 46, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 46, 201, 201, 201, 201, 201, 201, 201, 201, 201, 97, 46, 46, 46, 46, 10, 5, 5, 3, 3, 46, 46] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 423 number of broken/clashed sets: 5 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113980 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113980/1 /scratch/stefan/7770410/working/building/REAL300020113980 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1576) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1576 `/scratch/stefan/7770410/working/3D/1576' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CNC(C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113980.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113980 none CC(=O)NC1=CNC(C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 30, 30, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 32, 46, 46, 46, 46, 46, 11, 11, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 6, 1, 1, 1, 1, 11, 32, 32, 46, 46, 1, 1] 201 rigid atoms, others: [48, 39, 40, 41, 42, 12, 13, 14, 15, 16, 49, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 227 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113980 none CC(=O)NC1=CNC(C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 107, 107, 107, 107, 107, 34, 34, 34, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 107, 107, 107, 107, 107, 107, 107, 107, 107, 34, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [43, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 214 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113980 none CC(=O)NC1=CNC(C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 30, 30, 30, 107, 107, 107, 166, 201, 201, 201, 201, 201, 107, 107, 30, 2, 2, 2, 2, 1, 1, 2, 2, 2, 11, 30, 30, 30, 30, 107, 166, 166, 201, 201, 30, 30] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 707 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113980 none CC(=O)NC1=CNC(C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 98, 98, 98, 45, 45, 45, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 45, 201, 201, 201, 201, 201, 201, 201, 201, 201, 98, 45, 45, 45, 45, 9, 5, 5, 3, 3, 45, 45] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 425 number of broken/clashed sets: 5 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113980 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113980 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113980/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113980/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113980 Building REAL300020113981 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113981' /scratch/stefan/7770410/working/building/REAL300020113981 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113981 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113981/0 /scratch/stefan/7770410/working/building/REAL300020113981 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1577) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1577 `/scratch/stefan/7770410/working/3D/1577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CN=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113981.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113981 none CCC1=CN=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 21, 21, 21, 8, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 22, 35, 35, 35, 35, 35, 8, 8, 1, 34, 34, 34, 34, 34, 21, 21, 21, 6, 1, 1, 1, 1, 8, 22, 22, 35, 35, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 278 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113981 none CCC1=CN=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 78, 78, 78, 43, 78, 78, 25, 25, 25, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 116, 116, 116, 116, 116, 78, 78, 78, 25, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 472 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113981 none CCC1=CN=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 21, 21, 21, 78, 78, 78, 124, 156, 156, 156, 156, 156, 78, 78, 21, 3, 3, 3, 3, 3, 1, 1, 1, 9, 21, 21, 21, 21, 78, 124, 124, 156, 156, 21, 21] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 568 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113981 none CCC1=CN=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 156, 156, 156, 118, 156, 156, 70, 70, 70, 36, 36, 36, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 36, 201, 201, 201, 201, 201, 156, 156, 156, 70, 36, 36, 36, 36, 7, 4, 4, 2, 2, 36, 36] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 708 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113981 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113981/1 /scratch/stefan/7770410/working/building/REAL300020113981 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1578) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1578 `/scratch/stefan/7770410/working/3D/1578' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CN=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113981.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113981 none CCC1=CN=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 21, 21, 21, 8, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 23, 36, 36, 36, 36, 36, 8, 8, 1, 33, 33, 33, 33, 33, 21, 21, 21, 6, 1, 1, 1, 1, 8, 23, 23, 36, 36, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 275 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113981 none CCC1=CN=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 77, 77, 77, 42, 77, 77, 24, 24, 24, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 115, 115, 115, 115, 115, 77, 77, 77, 24, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 470 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113981 none CCC1=CN=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 21, 21, 21, 77, 77, 77, 125, 156, 156, 156, 156, 156, 77, 77, 21, 3, 3, 3, 3, 3, 1, 1, 1, 9, 21, 21, 21, 21, 77, 125, 125, 156, 156, 21, 21] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 569 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113981 none CCC1=CN=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 156, 156, 156, 119, 156, 156, 71, 71, 71, 37, 37, 37, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 37, 201, 201, 201, 201, 201, 156, 156, 156, 71, 37, 37, 37, 37, 8, 4, 4, 2, 2, 37, 37] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 706 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113981 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113981 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113981/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113981/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113981 Building REAL300020113982 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113982' /scratch/stefan/7770410/working/building/REAL300020113982 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113982 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113982/0 /scratch/stefan/7770410/working/building/REAL300020113982 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1579) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1579 `/scratch/stefan/7770410/working/3D/1579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOCC1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113982.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113982 none CCN1CCOCC1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 17, 17, 17, 17, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 55, 78, 97, 97, 97, 97, 13, 13, 1, 23, 23, 23, 23, 23, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 13, 55, 55, 78, 78, 1, 1] 201 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 49, 50, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 432 number of broken/clashed sets: 172 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113982 none CCN1CCOCC1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 88, 88, 88, 88, 88, 88, 54, 54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 13, 104, 104, 104, 104, 104, 88, 88, 88, 88, 88, 88, 88, 54, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13] 201 rigid atoms, others: [44, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 402 number of broken/clashed sets: 172 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113982 none CCN1CCOCC1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 88, 88, 88, 165, 196, 201, 201, 201, 201, 88, 88, 17, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 17, 17, 17, 17, 88, 165, 165, 196, 196, 17, 17] 201 rigid atoms, others: [32, 1, 2, 3, 4, 33, 6, 7, 8, 34, 35, 36, 38, 37, 5] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 687 number of broken/clashed sets: 172 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113982 none CCN1CCOCC1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 180, 180, 180, 97, 97, 97, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 97, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 180, 97, 97, 97, 97, 17, 6, 6, 4, 4, 97, 97] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 573 number of broken/clashed sets: 173 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113982 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113982/1 /scratch/stefan/7770410/working/building/REAL300020113982 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1580) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1580 `/scratch/stefan/7770410/working/3D/1580' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113982.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113982/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113982 none CCN1CCOCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 17, 17, 17, 17, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 55, 78, 97, 97, 97, 97, 13, 13, 1, 23, 23, 23, 23, 23, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 13, 55, 55, 78, 78, 1, 1] 201 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 49, 50, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 432 number of broken/clashed sets: 172 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113982 none CCN1CCOCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 88, 88, 88, 88, 88, 88, 54, 54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 13, 104, 104, 104, 104, 104, 88, 88, 88, 88, 88, 88, 88, 54, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13] 201 rigid atoms, others: [44, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 402 number of broken/clashed sets: 172 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113982 none CCN1CCOCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 88, 88, 88, 165, 196, 201, 201, 201, 201, 88, 88, 17, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 17, 17, 17, 17, 88, 165, 165, 196, 196, 17, 17] 201 rigid atoms, others: [32, 1, 2, 3, 4, 33, 6, 7, 8, 34, 35, 36, 38, 37, 5] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 687 number of broken/clashed sets: 172 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113982 none CCN1CCOCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 180, 180, 180, 98, 98, 98, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 98, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 180, 98, 98, 98, 98, 17, 6, 6, 4, 4, 98, 98] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 571 number of broken/clashed sets: 172 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113982 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113982 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113982/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113982/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113982 Building REAL300020113983 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113983' /scratch/stefan/7770410/working/building/REAL300020113983 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113983 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113983/0 /scratch/stefan/7770410/working/building/REAL300020113983 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1581) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1581 `/scratch/stefan/7770410/working/3D/1581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(F)CCCC1) `REAL300020113983.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113983 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(F)CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 15, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 7, 9, 9, 9, 9, 9, 1, 1, 13, 59, 161, 161, 161, 161, 161, 59, 13, 13, 13, 13, 1, 7, 7, 9, 9, 13, 13, 161, 161, 161, 161, 161, 161, 161, 161] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 476 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113983 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(F)CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 15, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 45, 45, 45, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 45, 118, 201, 201, 201, 201, 201, 118, 45, 45, 45, 45, 9, 4, 4, 2, 2, 45, 45, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 598 number of broken/clashed sets: 18 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113983 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(F)CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 15, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 32, 45, 45, 45, 45, 45, 13, 13, 1, 6, 40, 40, 40, 40, 40, 6, 1, 1, 1, 1, 13, 32, 32, 45, 45, 1, 1, 40, 40, 40, 40, 40, 40, 40, 40] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 35, 36, 26, 27, 28, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 275 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113983 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(F)CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 15, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 40, 40, 40, 161, 161, 161, 185, 201, 201, 201, 201, 201, 161, 161, 40, 1, 1, 1, 1, 1, 1, 10, 40, 40, 40, 40, 161, 185, 185, 201, 201, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 37, 38, 39, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 480 number of broken/clashed sets: 18 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113983 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113983/1 /scratch/stefan/7770410/working/building/REAL300020113983 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1582) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1582 `/scratch/stefan/7770410/working/3D/1582' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(F)CCCC1) `REAL300020113983.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113983/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113983 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(F)CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 15, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 7, 9, 9, 9, 9, 9, 1, 1, 13, 59, 163, 163, 163, 163, 163, 59, 13, 13, 13, 13, 1, 7, 7, 9, 9, 13, 13, 163, 163, 163, 163, 163, 163, 163, 163] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 480 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113983 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(F)CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 15, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 117, 45, 45, 45, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 45, 117, 201, 201, 201, 201, 201, 117, 45, 45, 45, 45, 9, 4, 4, 2, 2, 45, 45, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 596 number of broken/clashed sets: 18 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113983 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(F)CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 15, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 32, 45, 45, 45, 45, 45, 13, 13, 1, 6, 40, 40, 40, 40, 40, 6, 1, 1, 1, 1, 13, 32, 32, 45, 45, 1, 1, 40, 40, 40, 40, 40, 40, 40, 40] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 35, 36, 26, 27, 28, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 275 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113983 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(F)CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 15, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 40, 40, 40, 163, 163, 163, 187, 201, 201, 201, 201, 201, 163, 163, 40, 1, 1, 1, 1, 1, 1, 10, 40, 40, 40, 40, 163, 187, 187, 201, 201, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 37, 38, 39, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 470 number of broken/clashed sets: 18 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113983 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113983 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113983/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113983/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113983 Building REAL300020113984 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113984' /scratch/stefan/7770410/working/building/REAL300020113984 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113984 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113984/0 /scratch/stefan/7770410/working/building/REAL300020113984 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1583) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1583 `/scratch/stefan/7770410/working/3D/1583' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CN=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113984.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113984 none CCC1=CC=CN=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [18, 16, 16, 16, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 6, 4, 4, 1, 18, 18, 18, 18, 18, 16, 16, 16, 6, 1, 1, 1, 1, 4, 6, 6, 6, 6, 1, 1] 24 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113984 none CCC1=CC=CN=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [18, 16, 16, 16, 16, 16, 16, 8, 8, 8, 4, 4, 4, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 4, 18, 18, 18, 18, 18, 16, 16, 16, 8, 4, 4, 4, 4, 1, 5, 5, 5, 5, 4, 4] 24 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 62 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113984 none CCC1=CC=CN=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 16, 16, 16, 16, 16, 16, 21, 21, 21, 21, 21, 21, 16, 16, 16, 6, 6, 6, 6, 6, 1, 1, 1, 8, 16, 16, 16, 16, 16, 21, 21, 21, 21, 16, 16] 24 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113984 none CCC1=CC=CN=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 21, 21, 21, 21, 21, 21, 12, 12, 12, 6, 6, 6, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 24, 24, 24, 24, 24, 21, 21, 21, 12, 6, 6, 6, 6, 5, 3, 3, 1, 1, 6, 6] 24 rigid atoms, others: [43, 44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46]) total number of confs: 72 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113984 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113984/1 /scratch/stefan/7770410/working/building/REAL300020113984 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1584) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1584 `/scratch/stefan/7770410/working/3D/1584' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CN=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113984.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113984/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113984 none CCC1=CC=CN=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [18, 16, 16, 16, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 6, 4, 4, 1, 18, 18, 18, 18, 18, 16, 16, 16, 6, 1, 1, 1, 1, 4, 6, 6, 6, 6, 1, 1] 24 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113984 none CCC1=CC=CN=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [18, 16, 16, 16, 16, 16, 16, 8, 8, 8, 4, 4, 4, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 4, 18, 18, 18, 18, 18, 16, 16, 16, 8, 4, 4, 4, 4, 1, 5, 5, 5, 5, 4, 4] 24 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 62 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113984 none CCC1=CC=CN=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 16, 16, 16, 16, 16, 16, 21, 21, 21, 21, 21, 21, 16, 16, 16, 6, 6, 6, 6, 6, 1, 1, 1, 8, 16, 16, 16, 16, 16, 21, 21, 21, 21, 16, 16] 24 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113984 none CCC1=CC=CN=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 21, 21, 21, 21, 21, 21, 12, 12, 12, 6, 6, 6, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 24, 24, 24, 24, 24, 21, 21, 21, 12, 6, 6, 6, 6, 5, 3, 3, 1, 1, 6, 6] 24 rigid atoms, others: [43, 44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46]) total number of confs: 72 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113984 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113984 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113984/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113984/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113984 Building REAL300020113985 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113985' /scratch/stefan/7770410/working/building/REAL300020113985 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113985 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113985/0 /scratch/stefan/7770410/working/building/REAL300020113985 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1585) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1585 `/scratch/stefan/7770410/working/3D/1585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=COC2=CC(F)=CC=C12) `REAL300020113985.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113985 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=COC2=CC(F)=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 37, 102, 102, 102, 102, 102, 102, 102, 102, 102, 37, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 102, 102, 102, 102] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 218 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113985 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=COC2=CC(F)=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 124, 62, 62, 62, 12, 12, 12, 7, 4, 1, 1, 1, 1, 1, 1, 12, 12, 62, 124, 201, 201, 201, 201, 201, 201, 201, 201, 201, 124, 62, 62, 62, 62, 12, 7, 7, 4, 4, 62, 62, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 473 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113985 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=COC2=CC(F)=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 37, 53, 61, 61, 61, 61, 11, 11, 1, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 37, 37, 53, 53, 1, 1, 22, 22, 22, 22] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113985 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=COC2=CC(F)=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 22, 22, 22, 102, 102, 102, 163, 201, 201, 201, 201, 201, 102, 102, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 22, 22, 22, 22, 102, 163, 163, 201, 201, 22, 22, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 709 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113985 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113985/1 /scratch/stefan/7770410/working/building/REAL300020113985 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1586) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1586 `/scratch/stefan/7770410/working/3D/1586' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=COC2=CC(F)=CC=C12) `REAL300020113985.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113985/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113985 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=COC2=CC(F)=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 37, 101, 101, 101, 101, 101, 101, 101, 101, 101, 37, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 101, 101, 101, 101] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 217 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113985 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=COC2=CC(F)=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 124, 62, 62, 62, 12, 12, 12, 7, 4, 1, 1, 1, 1, 1, 1, 12, 12, 62, 124, 201, 201, 201, 201, 201, 201, 201, 201, 201, 124, 62, 62, 62, 62, 12, 7, 7, 4, 4, 62, 62, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 473 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113985 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=COC2=CC(F)=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 37, 53, 61, 61, 61, 61, 11, 11, 1, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 37, 37, 53, 53, 1, 1, 22, 22, 22, 22] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113985 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=COC2=CC(F)=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 22, 22, 22, 101, 101, 101, 163, 201, 201, 201, 201, 201, 101, 101, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 22, 22, 22, 22, 101, 163, 163, 201, 201, 22, 22, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 713 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113985 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113985 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113985/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113985/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113985 Building REAL300020113986 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113986' /scratch/stefan/7770410/working/building/REAL300020113986 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113986 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113986/0 /scratch/stefan/7770410/working/building/REAL300020113986 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1587) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1587 `/scratch/stefan/7770410/working/3D/1587' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN=C1) `REAL300020113986.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113986 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 25, 51, 25, 25, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 51, 110, 110, 110, 110, 110, 51, 51, 51, 51, 51, 51, 25, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8, 110, 110, 110, 110] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 313 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113986 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 72, 118, 72, 72, 37, 37, 37, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 37, 118, 201, 201, 201, 201, 201, 118, 118, 118, 118, 118, 118, 72, 37, 37, 37, 37, 8, 4, 4, 2, 2, 37, 37, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 628 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113986 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 24, 36, 36, 36, 36, 36, 8, 8, 1, 15, 34, 34, 34, 34, 34, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 8, 24, 24, 36, 36, 1, 1, 34, 34, 34, 34] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 44, 45, 21, 38, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47, 48, 49]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113986 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 14, 14, 14, 34, 34, 34, 110, 110, 110, 165, 201, 201, 201, 201, 201, 110, 110, 34, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 14, 34, 34, 34, 34, 110, 165, 165, 201, 201, 34, 34, 1, 1, 1, 1] 201 rigid atoms, others: [1, 46, 47, 48, 49, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 724 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113986 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113986/1 /scratch/stefan/7770410/working/building/REAL300020113986 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1588) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1588 `/scratch/stefan/7770410/working/3D/1588' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN=C1) `REAL300020113986.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113986/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113986 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 25, 51, 25, 25, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 51, 111, 111, 111, 111, 111, 51, 51, 51, 51, 51, 51, 25, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8, 111, 111, 111, 111] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 314 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113986 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 72, 118, 72, 72, 36, 36, 36, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 36, 118, 201, 201, 201, 201, 201, 118, 118, 118, 118, 118, 118, 72, 36, 36, 36, 36, 7, 4, 4, 2, 2, 36, 36, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 628 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113986 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 24, 36, 36, 36, 36, 36, 8, 8, 1, 15, 34, 34, 34, 34, 34, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 8, 24, 24, 36, 36, 1, 1, 34, 34, 34, 34] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 44, 45, 21, 38, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47, 48, 49]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113986 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 14, 14, 14, 34, 34, 34, 111, 111, 111, 165, 201, 201, 201, 201, 201, 111, 111, 34, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 14, 34, 34, 34, 34, 111, 165, 165, 201, 201, 34, 34, 1, 1, 1, 1] 201 rigid atoms, others: [1, 46, 47, 48, 49, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 722 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113986 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113986 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113986/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113986/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113986 Building REAL300020113987 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113987' /scratch/stefan/7770410/working/building/REAL300020113987 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113987 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113987/0 /scratch/stefan/7770410/working/building/REAL300020113987 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1589) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1589 `/scratch/stefan/7770410/working/3D/1589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=C2C=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CN12) `REAL300020113987.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113987 none CC1=NN=C2C=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 31, 47, 52, 52, 52, 52, 9, 9, 1, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 9, 31, 31, 47, 47, 1, 1, 15] 201 rigid atoms, others: [35, 36, 37, 38, 44, 10, 11, 12, 13, 14, 45, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46]) total number of confs: 232 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113987 none CC1=NN=C2C=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 72, 72, 72, 72, 30, 30, 30, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 72, 72, 72, 72, 72, 72, 72, 30, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9, 72] 201 rigid atoms, others: [39, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 174 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113987 none CC1=NN=C2C=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 72, 72, 72, 143, 201, 201, 201, 201, 201, 72, 72, 15, 1, 1, 2, 2, 2, 1, 1, 5, 15, 15, 15, 15, 72, 143, 143, 201, 201, 15, 15, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 46, 33, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 830 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113987 none CC1=NN=C2C=CC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 88, 88, 88, 54, 54, 54, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 54, 201, 201, 201, 201, 201, 201, 201, 88, 54, 54, 54, 54, 13, 6, 6, 4, 4, 54, 54, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 427 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113987 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113987/1 /scratch/stefan/7770410/working/building/REAL300020113987 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1590) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1590 `/scratch/stefan/7770410/working/3D/1590' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=C2C=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CN12) `REAL300020113987.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113987 none CC1=NN=C2C=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 31, 47, 52, 52, 52, 52, 9, 9, 1, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 9, 31, 31, 47, 47, 1, 1, 15] 201 rigid atoms, others: [35, 36, 37, 38, 44, 10, 11, 12, 13, 14, 45, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46]) total number of confs: 232 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113987 none CC1=NN=C2C=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 72, 72, 72, 72, 30, 30, 30, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 72, 72, 72, 72, 72, 72, 72, 30, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9, 72] 201 rigid atoms, others: [39, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 174 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113987 none CC1=NN=C2C=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 72, 72, 72, 143, 201, 201, 201, 201, 201, 72, 72, 15, 1, 1, 2, 2, 2, 1, 1, 5, 15, 15, 15, 15, 72, 143, 143, 201, 201, 15, 15, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 46, 33, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 830 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113987 none CC1=NN=C2C=CC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 88, 88, 88, 54, 54, 54, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 54, 201, 201, 201, 201, 201, 201, 201, 88, 54, 54, 54, 54, 12, 6, 6, 4, 4, 54, 54, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 428 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113987 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113987 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113987/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113987/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113987 Building REAL300020113988 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113988' /scratch/stefan/7770410/working/building/REAL300020113988 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113988 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113988/0 /scratch/stefan/7770410/working/building/REAL300020113988 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1591) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1591 `/scratch/stefan/7770410/working/3D/1591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)N1N=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1C) `REAL300020113988.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113988 none CCC(C)N1N=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 16, 8, 16, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 51, 68, 83, 83, 83, 83, 11, 11, 1, 8, 8, 8, 22, 22, 22, 22, 22, 16, 16, 16, 16, 6, 1, 1, 1, 1, 11, 51, 51, 68, 68, 1, 1, 8, 8, 8, 8] 201 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 48, 49, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50, 51, 52, 53]) total number of confs: 382 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113988 none CCC(C)N1N=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 78, 51, 78, 51, 51, 46, 46, 46, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 11, 51, 51, 51, 102, 102, 102, 102, 102, 78, 78, 78, 78, 46, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 51, 51, 51, 51] 201 rigid atoms, others: [43, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 457 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113988 none CCC(C)N1N=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 51, 51, 51, 123, 161, 173, 173, 173, 173, 51, 51, 8, 1, 1, 1, 6, 6, 6, 6, 6, 3, 4, 4, 4, 2, 8, 8, 8, 8, 51, 123, 123, 161, 161, 8, 8, 1, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 50, 26, 27, 28] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53]) total number of confs: 676 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113988 none CCC(C)N1N=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 173, 201, 173, 173, 170, 170, 170, 83, 83, 83, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 83, 173, 173, 173, 201, 201, 201, 201, 201, 201, 201, 201, 201, 170, 83, 83, 83, 83, 17, 6, 6, 4, 4, 83, 83, 173, 173, 173, 173] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 627 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113988 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113988/1 /scratch/stefan/7770410/working/building/REAL300020113988 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1592) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1592 `/scratch/stefan/7770410/working/3D/1592' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)N1N=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1C) `REAL300020113988.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113988/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113988 none CCC(C)N1N=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 16, 8, 16, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 51, 68, 83, 83, 83, 83, 11, 11, 1, 8, 8, 8, 22, 22, 22, 22, 22, 16, 16, 16, 16, 6, 1, 1, 1, 1, 11, 51, 51, 68, 68, 1, 1, 8, 8, 8, 8] 201 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 48, 49, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50, 51, 52, 53]) total number of confs: 382 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113988 none CCC(C)N1N=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 78, 51, 78, 51, 51, 46, 46, 46, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 11, 51, 51, 51, 102, 102, 102, 102, 102, 78, 78, 78, 78, 46, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 51, 51, 51, 51] 201 rigid atoms, others: [43, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 457 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113988 none CCC(C)N1N=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 51, 51, 51, 123, 161, 173, 173, 173, 173, 51, 51, 8, 1, 1, 1, 6, 6, 6, 6, 6, 3, 4, 4, 4, 2, 8, 8, 8, 8, 51, 123, 123, 161, 161, 8, 8, 1, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 50, 26, 27, 28] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53]) total number of confs: 676 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113988 none CCC(C)N1N=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 174, 201, 174, 174, 171, 171, 171, 84, 84, 84, 19, 19, 19, 6, 4, 1, 1, 1, 1, 1, 1, 19, 19, 84, 174, 174, 174, 201, 201, 201, 201, 201, 201, 201, 201, 201, 171, 84, 84, 84, 84, 19, 6, 6, 4, 4, 84, 84, 174, 174, 174, 174] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 621 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113988 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113988 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113988/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113988/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113988 Building REAL300020113989 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113989' /scratch/stefan/7770410/working/building/REAL300020113989 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113989 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113989/0 /scratch/stefan/7770410/working/building/REAL300020113989 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1593) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1593 `/scratch/stefan/7770410/working/3D/1593' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NO1) `REAL300020113989.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113989 none CN(C)CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 8, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 30, 45, 45, 45, 45, 45, 10, 10, 1, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 8, 6, 1, 1, 1, 1, 10, 30, 30, 45, 45, 1, 1] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 258 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113989 none CN(C)CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 40, 40, 40, 38, 38, 38, 10, 10, 10, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 10, 40, 40, 103, 103, 103, 103, 103, 103, 103, 103, 40, 38, 10, 10, 10, 10, 1, 5, 5, 7, 7, 10, 10] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 417 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113989 none CN(C)CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 5, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 40, 40, 40, 98, 127, 127, 127, 127, 127, 40, 40, 8, 1, 1, 5, 5, 5, 5, 5, 5, 4, 4, 1, 3, 8, 8, 8, 8, 40, 98, 98, 127, 127, 8, 8] 201 rigid atoms, others: [3, 36, 5, 6, 7, 4, 26, 27] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 513 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113989 none CN(C)CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 126, 126, 126, 124, 124, 124, 45, 45, 45, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 45, 126, 126, 201, 201, 201, 201, 201, 201, 201, 201, 126, 124, 45, 45, 45, 45, 7, 4, 4, 2, 2, 45, 45] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 794 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113989 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113989/1 /scratch/stefan/7770410/working/building/REAL300020113989 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1594) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1594 `/scratch/stefan/7770410/working/3D/1594' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NO1) `REAL300020113989.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113989 none CN(C)CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 8, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 30, 45, 45, 45, 45, 45, 10, 10, 1, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 8, 6, 1, 1, 1, 1, 10, 30, 30, 45, 45, 1, 1] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 258 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113989 none CN(C)CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 40, 40, 40, 38, 38, 38, 10, 10, 10, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 10, 40, 40, 103, 103, 103, 103, 103, 103, 103, 103, 40, 38, 10, 10, 10, 10, 1, 5, 5, 7, 7, 10, 10] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 417 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113989 none CN(C)CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 5, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 40, 40, 40, 98, 127, 127, 127, 127, 127, 40, 40, 8, 1, 1, 5, 5, 5, 5, 5, 5, 4, 4, 1, 3, 8, 8, 8, 8, 40, 98, 98, 127, 127, 8, 8] 201 rigid atoms, others: [3, 36, 5, 6, 7, 4, 26, 27] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 513 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113989 none CN(C)CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 127, 127, 127, 125, 125, 125, 45, 45, 45, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 45, 127, 127, 201, 201, 201, 201, 201, 201, 201, 201, 127, 125, 45, 45, 45, 45, 7, 4, 4, 2, 2, 45, 45] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 790 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113989 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113989 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113989/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113989/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113989 Building REAL300020113990 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113990' /scratch/stefan/7770410/working/building/REAL300020113990 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300020113990 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113990/0 /scratch/stefan/7770410/working/building/REAL300020113990 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1595) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1595 `/scratch/stefan/7770410/working/3D/1595' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CC2=CN=CN21) `REAL300020113990.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113990 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CC2=CN=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 37, 53, 61, 61, 61, 61, 11, 11, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 11, 37, 37, 53, 53, 1, 1, 21, 21, 21, 21] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 42, 43, 21] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 258 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113990 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CC2=CN=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 38, 38, 38, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 38, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 95, 95, 95, 95] 201 rigid atoms, others: [37, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 212 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113990 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CC2=CN=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 21, 21, 21, 95, 95, 95, 165, 201, 201, 201, 201, 201, 95, 95, 21, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 21, 21, 21, 21, 95, 165, 165, 201, 201, 21, 21, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 45, 46, 47, 22, 23, 24, 25, 26, 27, 28] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 737 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113990 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CC2=CN=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 136, 136, 136, 62, 62, 62, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 62, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 136, 62, 62, 62, 62, 10, 6, 6, 4, 4, 62, 62, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 509 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113990 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113990/1 /scratch/stefan/7770410/working/building/REAL300020113990 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1596) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1596 `/scratch/stefan/7770410/working/3D/1596' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CC2=C[NH+]=CN21) `REAL300020113990.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113990/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113990 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CC2=C[NH+]=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.cat', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 6, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 16, 18, 24, 24, 24, 24, 6, 6, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 6, 16, 16, 18, 18, 1, 1, 17, 17, 17, 17] 42 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 43, 44, 21, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48]) total number of confs: 100 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113990 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CC2=C[NH+]=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.cat', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 6, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 17, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 8, 12, 19, 19, 19, 19, 1, 1, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 17, 6, 6, 6, 6, 1, 8, 8, 12, 12, 6, 6, 29, 29, 29, 29] 42 rigid atoms, others: [38, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 127 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113990 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CC2=C[NH+]=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.cat', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 6, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 29, 29, 29, 42, 42, 42, 42, 42, 42, 29, 29, 17, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 17, 17, 17, 17, 29, 42, 42, 42, 42, 17, 17, 1, 1, 1, 1] 42 rigid atoms, others: [0, 1, 2, 3, 45, 46, 47, 48, 22, 23, 24, 25, 26, 27, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113990 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CC2=C[NH+]=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.cat', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 6, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 36, 36, 36, 25, 25, 25, 20, 20, 20, 7, 4, 1, 1, 1, 1, 1, 1, 20, 20, 25, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 36, 25, 25, 25, 25, 20, 7, 7, 4, 4, 25, 25, 42, 42, 42, 42] 42 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 119 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113990 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `2' /scratch/stefan/7770410/working/building/REAL300020113990/2 /scratch/stefan/7770410/working/building/REAL300020113990 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 2 (index: 1597) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1597 `/scratch/stefan/7770410/working/3D/1597' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CC2=CN=CN21) `REAL300020113990.mol2' -> `2.mol2' `temp.mol2' -> `REAL300020113990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113990/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113990 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CC2=CN=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 37, 53, 61, 61, 61, 61, 11, 11, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 11, 37, 37, 53, 53, 1, 1, 21, 21, 21, 21] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 42, 43, 21] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 258 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113990 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CC2=CN=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 39, 39, 39, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 39, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 96, 96, 96, 96] 201 rigid atoms, others: [37, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 216 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113990 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CC2=CN=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 21, 21, 21, 96, 96, 96, 166, 201, 201, 201, 201, 201, 96, 96, 21, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 21, 21, 21, 21, 96, 166, 166, 201, 201, 21, 21, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 45, 46, 47, 22, 23, 24, 25, 26, 27, 28] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 732 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113990 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CC2=CN=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 136, 136, 136, 61, 61, 61, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 61, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 136, 61, 61, 61, 61, 10, 6, 6, 4, 4, 61, 61, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 511 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113990 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113990 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 2: /scratch/stefan/7770410/working/building/REAL300020113990/2.* 1: /scratch/stefan/7770410/working/building/REAL300020113990/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113990/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113990 Building REAL300020113991 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113991' /scratch/stefan/7770410/working/building/REAL300020113991 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113991 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113991/0 /scratch/stefan/7770410/working/building/REAL300020113991 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1598) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1598 `/scratch/stefan/7770410/working/3D/1598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC(F)F)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113991.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113991 none O=C(NCC(F)F)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 7, 29, 29, 121, 156, 156, 7, 7, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 1, 1, 6, 29, 121, 121, 156, 7, 6, 6, 6, 6, 1, 6, 6, 6, 6, 6, 6] 201 rigid atoms, others: [35, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 651 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113991 none O=C(NCC(F)F)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 68, 77, 77, 201, 201, 201, 68, 68, 55, 55, 55, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 55, 77, 201, 201, 201, 68, 55, 55, 55, 55, 15, 6, 6, 4, 4, 55, 55] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 736 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113991 none O=C(NCC(F)F)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 4, 16, 16, 78, 116, 116, 4, 4, 1, 1, 1, 1, 1, 6, 6, 6, 22, 22, 24, 24, 24, 24, 6, 6, 1, 16, 78, 78, 116, 4, 1, 1, 1, 1, 6, 22, 22, 22, 22, 1, 1] 201 rigid atoms, others: [32, 33, 34, 40, 9, 10, 11, 12, 13, 41, 25, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) total number of confs: 545 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113991 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113991/1 /scratch/stefan/7770410/working/building/REAL300020113991 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1599) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1599 `/scratch/stefan/7770410/working/3D/1599' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC(F)F)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113991.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113991 none O=C(NCC(F)F)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 7, 28, 28, 119, 155, 155, 7, 7, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 1, 1, 6, 28, 119, 119, 155, 7, 6, 6, 6, 6, 1, 6, 6, 6, 6, 6, 6] 201 rigid atoms, others: [35, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 647 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113991 none O=C(NCC(F)F)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 67, 76, 76, 201, 201, 201, 67, 67, 54, 54, 54, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 54, 76, 201, 201, 201, 67, 54, 54, 54, 54, 15, 6, 6, 4, 4, 54, 54] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 737 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113991 none O=C(NCC(F)F)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 4, 16, 16, 78, 116, 116, 4, 4, 1, 1, 1, 1, 1, 6, 6, 6, 22, 22, 24, 24, 24, 24, 6, 6, 1, 16, 78, 78, 116, 4, 1, 1, 1, 1, 6, 22, 22, 22, 22, 1, 1] 201 rigid atoms, others: [32, 33, 34, 40, 9, 10, 11, 12, 13, 41, 25, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) total number of confs: 545 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113991 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113991 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113991/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113991/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113991 Building REAL300020113992 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113992' /scratch/stefan/7770410/working/building/REAL300020113992 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113992 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113992/0 /scratch/stefan/7770410/working/building/REAL300020113992 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1600) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1600 `/scratch/stefan/7770410/working/3D/1600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN(CCF)N=C1) `REAL300020113992.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113992 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN(CCF)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 15, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 19, 48, 48, 48, 115, 127, 48, 48, 19, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 48, 115, 115, 127, 127, 48] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 506 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113992 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN(CCF)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 15, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 33, 33, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 33, 50, 107, 107, 107, 201, 201, 107, 107, 50, 33, 33, 33, 33, 8, 4, 4, 2, 2, 33, 33, 107, 201, 201, 201, 201, 107] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 721 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113992 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN(CCF)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 15, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 22, 34, 34, 34, 34, 34, 8, 8, 1, 5, 11, 11, 11, 30, 37, 11, 11, 5, 1, 1, 1, 1, 8, 22, 22, 34, 34, 1, 1, 11, 30, 30, 37, 37, 11] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 288 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113992 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN(CCF)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 15, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 11, 11, 11, 48, 48, 48, 78, 107, 107, 107, 107, 107, 48, 48, 11, 1, 1, 1, 1, 5, 7, 1, 1, 5, 11, 11, 11, 11, 48, 78, 78, 107, 107, 11, 11, 1, 5, 5, 7, 7, 1] 201 rigid atoms, others: [1, 39, 44, 19, 20, 21, 22, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43]) total number of confs: 429 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113992 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113992/1 /scratch/stefan/7770410/working/building/REAL300020113992 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1601) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1601 `/scratch/stefan/7770410/working/3D/1601' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN(CCF)N=C1) `REAL300020113992.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113992 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN(CCF)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 15, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 19, 49, 49, 49, 116, 128, 49, 49, 19, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 49, 116, 116, 128, 128, 49] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 507 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113992 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN(CCF)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 15, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 33, 33, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 33, 50, 107, 107, 107, 201, 201, 107, 107, 50, 33, 33, 33, 33, 8, 4, 4, 2, 2, 33, 33, 107, 201, 201, 201, 201, 107] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 724 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113992 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN(CCF)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 15, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 22, 34, 34, 34, 34, 34, 8, 8, 1, 5, 11, 11, 11, 30, 37, 11, 11, 5, 1, 1, 1, 1, 8, 22, 22, 34, 34, 1, 1, 11, 30, 30, 37, 37, 11] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 288 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113992 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN(CCF)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 15, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 11, 11, 11, 49, 49, 49, 79, 108, 108, 108, 108, 108, 49, 49, 11, 1, 1, 1, 1, 5, 7, 1, 1, 5, 11, 11, 11, 11, 49, 79, 79, 108, 108, 11, 11, 1, 5, 5, 7, 7, 1] 201 rigid atoms, others: [1, 39, 44, 19, 20, 21, 22, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43]) total number of confs: 430 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113992 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113992 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113992/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113992/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113992 Building REAL300020113993 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113993' /scratch/stefan/7770410/working/building/REAL300020113993 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113993 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113993/0 /scratch/stefan/7770410/working/building/REAL300020113993 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1602) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1602 `/scratch/stefan/7770410/working/3D/1602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020113993.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113993 none CC1=CC(C)=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 27, 27, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 32, 45, 45, 45, 45, 45, 13, 13, 1, 27, 27, 27, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 13, 32, 32, 45, 45, 1, 1, 27] 155 rigid atoms, others: [45, 35, 36, 37, 38, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46]) total number of confs: 223 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113993 none CC1=CC(C)=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 115, 115, 115, 115, 60, 60, 60, 13, 13, 13, 1, 1, 1, 1, 1, 7, 9, 9, 9, 9, 9, 1, 1, 13, 115, 115, 115, 115, 115, 115, 115, 115, 60, 13, 13, 13, 13, 1, 7, 7, 9, 9, 13, 13, 115] 155 rigid atoms, others: [39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 265 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113993 none CC1=CC(C)=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 27, 27, 27, 115, 115, 115, 146, 155, 155, 155, 155, 155, 115, 115, 27, 1, 2, 2, 2, 1, 2, 2, 2, 12, 27, 27, 27, 27, 115, 146, 146, 155, 155, 27, 27, 1] 155 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 46, 26, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 404 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113993 none CC1=CC(C)=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 156, 156, 156, 156, 112, 112, 112, 45, 45, 45, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 45, 156, 156, 156, 156, 156, 156, 156, 156, 112, 45, 45, 45, 45, 9, 4, 4, 2, 2, 45, 45, 156] 156 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 386 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113993 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113993/1 /scratch/stefan/7770410/working/building/REAL300020113993 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1603) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1603 `/scratch/stefan/7770410/working/3D/1603' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020113993.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113993 none CC1=CC(C)=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 27, 27, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 31, 44, 44, 44, 44, 44, 13, 13, 1, 27, 27, 27, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 13, 31, 31, 44, 44, 1, 1, 27] 152 rigid atoms, others: [45, 35, 36, 37, 38, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46]) total number of confs: 220 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113993 none CC1=CC(C)=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 115, 115, 115, 115, 60, 60, 60, 13, 13, 13, 1, 1, 1, 1, 1, 7, 9, 9, 9, 9, 9, 1, 1, 13, 115, 115, 115, 115, 115, 115, 115, 115, 60, 13, 13, 13, 13, 1, 7, 7, 9, 9, 13, 13, 115] 152 rigid atoms, others: [39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 265 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113993 none CC1=CC(C)=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 27, 27, 27, 115, 115, 115, 144, 152, 152, 152, 152, 152, 115, 115, 27, 1, 2, 2, 2, 1, 2, 2, 2, 12, 27, 27, 27, 27, 115, 144, 144, 152, 152, 27, 27, 1] 152 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 46, 26, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 392 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113993 none CC1=CC(C)=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [152, 152, 152, 152, 152, 152, 109, 109, 109, 44, 44, 44, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 44, 152, 152, 152, 152, 152, 152, 152, 152, 109, 44, 44, 44, 44, 9, 4, 4, 2, 2, 44, 44, 152] 152 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 372 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113993 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113993 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113993/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113993/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113993 Building REAL300020113994 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113994' /scratch/stefan/7770410/working/building/REAL300020113994 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113994 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113994/0 /scratch/stefan/7770410/working/building/REAL300020113994 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1604) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1604 `/scratch/stefan/7770410/working/3D/1604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=NC=NN21) `REAL300020113994.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113994 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=NC=NN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 12, 52, 89, 89, 89, 89, 89, 89, 89, 89, 52, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 89, 89, 89, 89] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 238 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113994 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=NC=NN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [191, 191, 103, 103, 103, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 103, 191, 201, 201, 201, 201, 201, 201, 201, 201, 191, 103, 103, 103, 103, 18, 6, 6, 4, 4, 103, 103, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 543 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113994 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=NC=NN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 63, 82, 103, 103, 103, 103, 12, 12, 1, 6, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 12, 63, 63, 82, 82, 1, 1, 20, 20, 20, 20] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 386 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113994 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=NC=NN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 20, 20, 20, 89, 89, 89, 176, 201, 201, 201, 201, 201, 89, 89, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 20, 20, 20, 20, 89, 176, 176, 201, 201, 20, 20, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 708 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113994 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113994/1 /scratch/stefan/7770410/working/building/REAL300020113994 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1605) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1605 `/scratch/stefan/7770410/working/3D/1605' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=NC=NN21) `REAL300020113994.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113994/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113994 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=NC=NN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 12, 52, 89, 89, 89, 89, 89, 89, 89, 89, 52, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 89, 89, 89, 89] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 237 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113994 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=NC=NN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [192, 192, 101, 101, 101, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 101, 192, 201, 201, 201, 201, 201, 201, 201, 201, 192, 101, 101, 101, 101, 17, 6, 6, 4, 4, 101, 101, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 550 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113994 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=NC=NN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 63, 82, 101, 101, 101, 101, 12, 12, 1, 6, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 12, 63, 63, 82, 82, 1, 1, 18, 18, 18, 18] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 380 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113994 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=NC=NN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 18, 18, 18, 89, 89, 89, 177, 201, 201, 201, 201, 201, 89, 89, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 18, 18, 18, 18, 89, 177, 177, 201, 201, 18, 18, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 696 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113994 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113994 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113994/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113994/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113994 Building REAL300020113995 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113995' /scratch/stefan/7770410/working/building/REAL300020113995 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113995 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113995/0 /scratch/stefan/7770410/working/building/REAL300020113995 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1606) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1606 `/scratch/stefan/7770410/working/3D/1606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=NC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113995.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113995 none CN1C=NC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 54, 73, 94, 94, 94, 94, 12, 12, 1, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 12, 54, 54, 73, 73, 1, 1] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 40, 41, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) total number of confs: 360 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113995 none CN1C=NC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 102, 102, 48, 48, 48, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 12, 102, 102, 102, 102, 102, 48, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12] 201 rigid atoms, others: [35, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 248 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113995 none CN1C=NC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 21, 21, 21, 102, 102, 102, 168, 201, 201, 201, 201, 201, 102, 102, 21, 2, 2, 2, 1, 1, 8, 21, 21, 21, 21, 102, 168, 168, 201, 201, 21, 21] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 690 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113995 none CN1C=NC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 174, 174, 174, 96, 96, 96, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 96, 201, 201, 201, 201, 201, 174, 96, 96, 96, 96, 18, 6, 6, 4, 4, 96, 96] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 535 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113995 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113995/1 /scratch/stefan/7770410/working/building/REAL300020113995 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1607) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1607 `/scratch/stefan/7770410/working/3D/1607' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=NC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113995.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113995/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113995 none CN1C=NC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 53, 72, 94, 94, 94, 94, 12, 12, 1, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 12, 53, 53, 72, 72, 1, 1] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 40, 41, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) total number of confs: 358 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113995 none CN1C=NC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 103, 103, 48, 48, 48, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 17, 17, 17, 17, 1, 1, 12, 103, 103, 103, 103, 103, 48, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12] 201 rigid atoms, others: [35, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 253 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113995 none CN1C=NC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 20, 20, 20, 103, 103, 103, 169, 201, 201, 201, 201, 201, 103, 103, 20, 2, 2, 2, 1, 1, 8, 20, 20, 20, 20, 103, 169, 169, 201, 201, 20, 20] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 682 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113995 none CN1C=NC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 174, 174, 174, 94, 94, 94, 16, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 94, 201, 201, 201, 201, 201, 174, 94, 94, 94, 94, 16, 6, 6, 4, 4, 94, 94] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 539 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113995 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113995 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113995/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113995/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113995 Building REAL300020113996 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113996' /scratch/stefan/7770410/working/building/REAL300020113996 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113996 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113996/0 /scratch/stefan/7770410/working/building/REAL300020113996 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1608) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1608 `/scratch/stefan/7770410/working/3D/1608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=CC=CN=C21) `REAL300020113996.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113996 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=CC=CN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 12, 50, 101, 101, 101, 101, 101, 101, 101, 101, 101, 50, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 101, 101, 101, 101, 101, 101] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 252 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113996 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=CC=CN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [186, 186, 102, 102, 102, 20, 20, 20, 6, 4, 1, 1, 1, 1, 1, 1, 20, 20, 102, 186, 201, 201, 201, 201, 201, 201, 201, 201, 201, 186, 102, 102, 102, 102, 20, 6, 6, 4, 4, 102, 102, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 538 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113996 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=CC=CN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 67, 85, 100, 100, 100, 100, 12, 12, 1, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 12, 67, 67, 85, 85, 1, 1, 19, 19, 19, 19, 19, 19] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 376 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113996 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=CC=CN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 19, 19, 19, 101, 101, 101, 184, 201, 201, 201, 201, 201, 101, 101, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 19, 19, 19, 19, 101, 184, 184, 201, 201, 19, 19, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 663 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113996 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113996/1 /scratch/stefan/7770410/working/building/REAL300020113996 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1609) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1609 `/scratch/stefan/7770410/working/3D/1609' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=CC=CN=C21) `REAL300020113996.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113996 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=CC=CN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 12, 50, 101, 101, 101, 101, 101, 101, 101, 101, 101, 50, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 101, 101, 101, 101, 101, 101] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 252 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113996 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=CC=CN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [186, 186, 102, 102, 102, 20, 20, 20, 6, 4, 1, 1, 1, 1, 1, 1, 20, 20, 102, 186, 201, 201, 201, 201, 201, 201, 201, 201, 201, 186, 102, 102, 102, 102, 20, 6, 6, 4, 4, 102, 102, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 538 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113996 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=CC=CN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 67, 85, 100, 100, 100, 100, 12, 12, 1, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 12, 67, 67, 85, 85, 1, 1, 19, 19, 19, 19, 19, 19] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 376 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113996 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=CC=CN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 19, 19, 19, 101, 101, 101, 184, 201, 201, 201, 201, 201, 101, 101, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 19, 19, 19, 19, 101, 184, 184, 201, 201, 19, 19, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 663 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113996 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113996 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113996/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113996/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113996 Building REAL300020113997 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113997' /scratch/stefan/7770410/working/building/REAL300020113997 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113997 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113997/0 /scratch/stefan/7770410/working/building/REAL300020113997 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1610) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1610 `/scratch/stefan/7770410/working/3D/1610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CC=C(F)C=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113997.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113997 none O=C(CCC1=CC=C(F)C=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 23, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 8, 8, 8, 25, 38, 39, 39, 39, 39, 8, 8, 1, 23, 23, 29, 29, 29, 29, 29, 29, 5, 1, 1, 1, 1, 8, 25, 25, 38, 38, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 273 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113997 none O=C(CCC1=CC=C(F)C=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 101, 117, 117, 117, 117, 117, 117, 117, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 101, 101, 117, 117, 117, 117, 117, 117, 21, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 470 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113997 none O=C(CCC1=CC=C(F)C=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 14, 29, 29, 29, 117, 117, 117, 171, 201, 201, 201, 201, 201, 117, 117, 29, 3, 3, 1, 1, 1, 1, 1, 1, 14, 29, 29, 29, 29, 117, 171, 171, 201, 201, 29, 29] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 35, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 680 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113997 none O=C(CCC1=CC=C(F)C=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 185, 201, 201, 201, 201, 201, 201, 201, 40, 40, 40, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 40, 185, 185, 201, 201, 201, 201, 201, 201, 71, 40, 40, 40, 40, 10, 5, 5, 3, 3, 40, 40] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 776 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113997 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113997/1 /scratch/stefan/7770410/working/building/REAL300020113997 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1611) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1611 `/scratch/stefan/7770410/working/3D/1611' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CC=C(F)C=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113997.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113997/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113997 none O=C(CCC1=CC=C(F)C=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 23, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 8, 8, 8, 25, 38, 39, 39, 39, 39, 8, 8, 1, 23, 23, 29, 29, 29, 29, 29, 29, 5, 1, 1, 1, 1, 8, 25, 25, 38, 38, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 273 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113997 none O=C(CCC1=CC=C(F)C=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 99, 115, 115, 115, 115, 115, 115, 115, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 99, 99, 115, 115, 115, 115, 115, 115, 21, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 464 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113997 none O=C(CCC1=CC=C(F)C=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 14, 29, 29, 29, 115, 115, 115, 170, 201, 201, 201, 201, 201, 115, 115, 29, 3, 3, 1, 1, 1, 1, 1, 1, 14, 29, 29, 29, 29, 115, 170, 170, 201, 201, 29, 29] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 35, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 684 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113997 none O=C(CCC1=CC=C(F)C=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 187, 201, 201, 201, 201, 201, 201, 201, 39, 39, 39, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 39, 187, 187, 201, 201, 201, 201, 201, 201, 70, 39, 39, 39, 39, 9, 5, 5, 3, 3, 39, 39] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 771 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113997 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113997 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113997/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113997/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113997 Building REAL300020113998 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113998' /scratch/stefan/7770410/working/building/REAL300020113998 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113998 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113998/0 /scratch/stefan/7770410/working/building/REAL300020113998 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1612) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1612 `/scratch/stefan/7770410/working/3D/1612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CC=CN=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020113998.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113998 none O=C(CCC1=CC=CN=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 22, 28, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 8, 8, 8, 19, 31, 31, 31, 31, 31, 8, 8, 1, 22, 22, 28, 28, 45, 45, 45, 45, 5, 1, 1, 1, 1, 8, 19, 19, 31, 31, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 272 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113998 none O=C(CCC1=CC=CN=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 66, 84, 134, 134, 134, 134, 134, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 66, 66, 84, 84, 134, 134, 134, 134, 19, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 466 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113998 none O=C(CCC1=CC=CN=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 5, 3, 1, 1, 1, 1, 1, 1, 1, 23, 23, 45, 45, 45, 134, 134, 134, 173, 201, 201, 201, 201, 201, 134, 134, 45, 5, 5, 3, 3, 1, 1, 1, 1, 23, 45, 45, 45, 45, 134, 173, 173, 201, 201, 45, 45] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 657 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113998 none O=C(CCC1=CC=CN=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 107, 125, 201, 201, 201, 201, 201, 31, 31, 31, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 31, 107, 107, 125, 125, 201, 201, 201, 201, 48, 31, 31, 31, 31, 7, 4, 4, 2, 2, 31, 31] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 645 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113998 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113998/1 /scratch/stefan/7770410/working/building/REAL300020113998 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1613) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1613 `/scratch/stefan/7770410/working/3D/1613' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CC=CN=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020113998.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113998 none O=C(CCC1=CC=CN=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 22, 28, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 8, 8, 8, 19, 31, 31, 31, 31, 31, 8, 8, 1, 22, 22, 28, 28, 45, 45, 45, 45, 5, 1, 1, 1, 1, 8, 19, 19, 31, 31, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 272 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113998 none O=C(CCC1=CC=CN=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 67, 84, 133, 133, 133, 133, 133, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 67, 67, 84, 84, 133, 133, 133, 133, 19, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 461 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113998 none O=C(CCC1=CC=CN=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 5, 3, 1, 1, 1, 1, 1, 1, 1, 23, 23, 45, 45, 45, 133, 133, 133, 173, 201, 201, 201, 201, 201, 133, 133, 45, 5, 5, 3, 3, 1, 1, 1, 1, 23, 45, 45, 45, 45, 133, 173, 173, 201, 201, 45, 45] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 662 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113998 none O=C(CCC1=CC=CN=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 108, 126, 201, 201, 201, 201, 201, 31, 31, 31, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 31, 108, 108, 126, 126, 201, 201, 201, 201, 48, 31, 31, 31, 31, 7, 4, 4, 2, 2, 31, 31] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 646 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113998 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113998 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113998/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113998/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113998 Building REAL300020113999 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020113999' /scratch/stefan/7770410/working/building/REAL300020113999 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020113999 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020113999/0 /scratch/stefan/7770410/working/building/REAL300020113999 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1614) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1614 `/scratch/stefan/7770410/working/3D/1614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(F)=C1) `REAL300020113999.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020113999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113999 none COC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 12, 6, 12, 12, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 41, 55, 61, 61, 61, 61, 11, 11, 1, 12, 12, 12, 22, 22, 22, 12, 12, 6, 1, 1, 1, 1, 11, 41, 41, 55, 55, 1, 1, 12] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45]) total number of confs: 291 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113999 none COC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 75, 41, 75, 75, 41, 41, 41, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 75, 75, 75, 105, 105, 105, 75, 75, 41, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 75] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 391 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113999 none COC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 75, 75, 75, 145, 193, 201, 201, 201, 201, 75, 75, 12, 1, 1, 1, 3, 3, 3, 1, 1, 4, 12, 12, 12, 12, 75, 145, 145, 193, 193, 12, 12, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 45, 25, 26, 27, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 750 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113999 none COC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 138, 201, 201, 138, 138, 138, 59, 59, 59, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 59, 201, 201, 201, 201, 201, 201, 201, 201, 138, 59, 59, 59, 59, 13, 6, 6, 4, 4, 59, 59, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 776 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113999 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020113999/1 /scratch/stefan/7770410/working/building/REAL300020113999 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1615) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1615 `/scratch/stefan/7770410/working/3D/1615' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(F)=C1) `REAL300020113999.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020113999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020113999/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113999 none COC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 12, 6, 12, 12, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 40, 55, 61, 61, 61, 61, 11, 11, 1, 12, 12, 12, 22, 22, 22, 12, 12, 6, 1, 1, 1, 1, 11, 40, 40, 55, 55, 1, 1, 12] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45]) total number of confs: 291 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113999 none COC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 74, 40, 74, 74, 40, 40, 40, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 74, 74, 74, 105, 105, 105, 74, 74, 40, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 74] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 391 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113999 none COC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 74, 74, 74, 144, 192, 201, 201, 201, 201, 74, 74, 12, 1, 1, 1, 3, 3, 3, 1, 1, 4, 12, 12, 12, 12, 74, 144, 144, 192, 192, 12, 12, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 45, 25, 26, 27, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 751 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020113999 none COC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 138, 201, 201, 138, 138, 138, 58, 58, 58, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 58, 201, 201, 201, 201, 201, 201, 201, 201, 138, 58, 58, 58, 58, 12, 6, 6, 4, 4, 58, 58, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 779 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020113999 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020113999 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020113999/1.* 0: /scratch/stefan/7770410/working/building/REAL300020113999/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020113999 Building REAL300020114000 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114000' /scratch/stefan/7770410/working/building/REAL300020114000 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114000 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114000/0 /scratch/stefan/7770410/working/building/REAL300020114000 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1616) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1616 `/scratch/stefan/7770410/working/3D/1616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CC=CC=C2S1) `REAL300020114000.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114000 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 12, 51, 99, 99, 99, 99, 99, 99, 99, 99, 51, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 99, 99, 99, 99, 99] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 244 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114000 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 87, 87, 87, 16, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 87, 156, 201, 201, 201, 201, 201, 201, 201, 201, 156, 87, 87, 87, 87, 16, 6, 6, 4, 4, 87, 87, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 516 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114000 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 52, 70, 86, 86, 86, 86, 12, 12, 1, 6, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 12, 52, 52, 70, 70, 1, 1, 22, 22, 22, 22, 22] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 335 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114000 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 22, 22, 22, 99, 99, 99, 160, 201, 201, 201, 201, 201, 99, 99, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 22, 22, 22, 22, 99, 160, 160, 201, 201, 22, 22, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 718 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114000 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114000/1 /scratch/stefan/7770410/working/building/REAL300020114000 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1617) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1617 `/scratch/stefan/7770410/working/3D/1617' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CC=CC=C2S1) `REAL300020114000.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114000 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 12, 51, 102, 102, 102, 102, 102, 102, 102, 102, 51, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 102, 102, 102, 102, 102] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 247 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114000 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 87, 87, 87, 16, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 87, 156, 201, 201, 201, 201, 201, 201, 201, 201, 156, 87, 87, 87, 87, 16, 6, 6, 4, 4, 87, 87, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 516 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114000 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 52, 70, 86, 86, 86, 86, 12, 12, 1, 6, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 12, 52, 52, 70, 70, 1, 1, 22, 22, 22, 22, 22] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 335 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114000 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 22, 22, 22, 102, 102, 102, 160, 201, 201, 201, 201, 201, 102, 102, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 22, 22, 22, 22, 102, 160, 160, 201, 201, 22, 22, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 704 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114000 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114000 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114000/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114000/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114000 Building REAL300020114001 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114001' /scratch/stefan/7770410/working/building/REAL300020114001 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114001 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114001/0 /scratch/stefan/7770410/working/building/REAL300020114001 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1618) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1618 `/scratch/stefan/7770410/working/3D/1618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CNC2=CC=CC=C12) `REAL300020114001.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114001 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CNC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 8, 8, 8, 1, 1, 1, 1, 1, 9, 14, 20, 20, 20, 20, 1, 1, 8, 28, 88, 88, 88, 88, 88, 88, 88, 88, 28, 8, 8, 8, 8, 1, 9, 9, 14, 14, 8, 8, 88, 88, 88, 88, 88, 88] 187 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 222 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114001 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CNC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [140, 140, 77, 77, 77, 30, 30, 30, 8, 4, 1, 1, 1, 1, 1, 1, 30, 30, 77, 140, 187, 187, 187, 187, 187, 187, 187, 187, 140, 77, 77, 77, 77, 30, 8, 8, 4, 4, 77, 77, 187, 187, 187, 187, 187, 187] 187 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 477 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114001 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CNC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 38, 51, 68, 68, 68, 68, 8, 8, 1, 6, 32, 32, 32, 32, 32, 32, 32, 32, 6, 1, 1, 1, 1, 8, 38, 38, 51, 51, 1, 1, 32, 32, 32, 32, 32, 32] 187 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114001 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CNC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 32, 32, 32, 88, 88, 88, 167, 187, 187, 187, 187, 187, 88, 88, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 32, 32, 32, 32, 88, 167, 167, 187, 187, 32, 32, 1, 1, 1, 1, 1, 1] 187 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 652 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114001 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114001/1 /scratch/stefan/7770410/working/building/REAL300020114001 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1619) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1619 `/scratch/stefan/7770410/working/3D/1619' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CNC2=CC=CC=C12) `REAL300020114001.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114001 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CNC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 8, 8, 8, 1, 1, 1, 1, 1, 9, 14, 20, 20, 20, 20, 1, 1, 8, 27, 86, 86, 86, 86, 86, 86, 86, 86, 27, 8, 8, 8, 8, 1, 9, 9, 14, 14, 8, 8, 86, 86, 86, 86, 86, 86] 185 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 216 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114001 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CNC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [138, 138, 77, 77, 77, 30, 30, 30, 8, 4, 1, 1, 1, 1, 1, 1, 30, 30, 77, 138, 185, 185, 185, 185, 185, 185, 185, 185, 138, 77, 77, 77, 77, 30, 8, 8, 4, 4, 77, 77, 185, 185, 185, 185, 185, 185] 185 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 474 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114001 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CNC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 37, 50, 67, 67, 67, 67, 8, 8, 1, 6, 32, 32, 32, 32, 32, 32, 32, 32, 6, 1, 1, 1, 1, 8, 37, 37, 50, 50, 1, 1, 32, 32, 32, 32, 32, 32] 185 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114001 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CNC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 32, 32, 32, 86, 86, 86, 165, 185, 185, 185, 185, 185, 86, 86, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 32, 32, 32, 32, 86, 165, 165, 185, 185, 32, 32, 1, 1, 1, 1, 1, 1] 185 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 650 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114001 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114001 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114001/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114001/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114001 Building REAL300020114002 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114002' /scratch/stefan/7770410/working/building/REAL300020114002 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114002 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114002/0 /scratch/stefan/7770410/working/building/REAL300020114002 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1620) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1620 `/scratch/stefan/7770410/working/3D/1620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC2=NC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CN2C=C1) `REAL300020114002.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114002 none CC1=CC2=NC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CN2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 67, 88, 111, 111, 111, 111, 13, 13, 1, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 13, 67, 67, 88, 88, 1, 1, 17, 17, 17] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 409 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114002 none CC1=CC2=NC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CN2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 83, 83, 53, 53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 20, 20, 20, 20, 1, 1, 13, 83, 83, 83, 83, 83, 83, 83, 83, 53, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 83, 83, 83] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 248 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114002 none CC1=CC2=NC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CN2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 83, 83, 83, 162, 201, 201, 201, 201, 201, 83, 83, 17, 1, 1, 1, 1, 2, 2, 2, 1, 6, 17, 17, 17, 17, 83, 162, 162, 201, 201, 17, 17, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 45, 46, 47, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 714 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114002 none CC1=CC2=NC(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CN2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 193, 193, 193, 112, 112, 112, 24, 24, 24, 6, 4, 1, 1, 1, 1, 1, 1, 24, 24, 112, 201, 201, 201, 201, 201, 201, 201, 201, 193, 112, 112, 112, 112, 24, 6, 6, 4, 4, 112, 112, 201, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 539 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114002 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114002/1 /scratch/stefan/7770410/working/building/REAL300020114002 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1621) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1621 `/scratch/stefan/7770410/working/3D/1621' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC2=NC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CN2C=C1) `REAL300020114002.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114002 none CC1=CC2=NC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CN2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 67, 88, 113, 113, 113, 113, 13, 13, 1, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 13, 67, 67, 88, 88, 1, 1, 17, 17, 17] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 413 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114002 none CC1=CC2=NC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CN2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 85, 85, 53, 53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 20, 20, 20, 20, 1, 1, 13, 85, 85, 85, 85, 85, 85, 85, 85, 53, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 85, 85, 85] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 250 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114002 none CC1=CC2=NC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CN2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 85, 85, 85, 163, 201, 201, 201, 201, 201, 85, 85, 17, 1, 1, 1, 1, 2, 2, 2, 1, 6, 17, 17, 17, 17, 85, 163, 163, 201, 201, 17, 17, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 45, 46, 47, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 708 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114002 none CC1=CC2=NC(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CN2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 193, 193, 193, 110, 110, 110, 24, 24, 24, 6, 4, 1, 1, 1, 1, 1, 1, 24, 24, 110, 201, 201, 201, 201, 201, 201, 201, 201, 193, 110, 110, 110, 110, 24, 6, 6, 4, 4, 110, 110, 201, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 543 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114002 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114002 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114002/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114002/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114002 Building REAL300020114003 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114003' /scratch/stefan/7770410/working/building/REAL300020114003 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114003 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114003/0 /scratch/stefan/7770410/working/building/REAL300020114003 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1622) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1622 `/scratch/stefan/7770410/working/3D/1622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1C=CC(=O)NC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114003.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114003 none O=C(CN1C=CC(=O)NC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 11, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 31, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 8, 8, 8, 31, 44, 48, 48, 48, 48, 8, 8, 1, 31, 31, 33, 33, 33, 5, 1, 1, 1, 1, 8, 31, 31, 44, 44, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 44, 11, 12, 13, 14, 15, 43, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 289 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114003 none O=C(CN1C=CC(=O)NC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 11, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 111, 113, 113, 113, 113, 113, 113, 113, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 8, 111, 111, 113, 113, 113, 24, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [38, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 419 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114003 none O=C(CN1C=CC(=O)NC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 11, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 33, 33, 33, 113, 113, 113, 183, 201, 201, 201, 201, 201, 113, 113, 33, 2, 2, 1, 1, 1, 13, 33, 33, 33, 33, 113, 183, 183, 201, 201, 33, 33] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 658 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114003 none O=C(CN1C=CC(=O)NC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 11, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 201, 201, 201, 201, 201, 201, 201, 201, 47, 47, 47, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 47, 201, 201, 201, 201, 201, 92, 47, 47, 47, 47, 10, 6, 6, 4, 4, 47, 47] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 748 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114003 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114003/1 /scratch/stefan/7770410/working/building/REAL300020114003 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1623) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1623 `/scratch/stefan/7770410/working/3D/1623' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1C=CC(=O)NC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114003.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114003 none O=C(CN1C=CC(=O)NC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 11, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 31, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 8, 8, 8, 30, 43, 47, 47, 47, 47, 8, 8, 1, 31, 31, 34, 34, 34, 5, 1, 1, 1, 1, 8, 30, 30, 43, 43, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 44, 11, 12, 13, 14, 15, 43, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 288 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114003 none O=C(CN1C=CC(=O)NC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 11, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 111, 113, 113, 113, 113, 113, 113, 113, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 8, 111, 111, 113, 113, 113, 24, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [38, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 419 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114003 none O=C(CN1C=CC(=O)NC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 11, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 34, 34, 34, 113, 113, 113, 183, 201, 201, 201, 201, 201, 113, 113, 34, 2, 2, 1, 1, 1, 14, 34, 34, 34, 34, 113, 183, 183, 201, 201, 34, 34] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 658 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114003 none O=C(CN1C=CC(=O)NC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 11, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 201, 201, 201, 201, 201, 201, 201, 201, 48, 48, 48, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 48, 201, 201, 201, 201, 201, 93, 48, 48, 48, 48, 11, 6, 6, 4, 4, 48, 48] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 747 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114003 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114003 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114003/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114003/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114003 Building REAL300020114004 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114004' /scratch/stefan/7770410/working/building/REAL300020114004 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114004 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114004/0 /scratch/stefan/7770410/working/building/REAL300020114004 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1624) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1624 `/scratch/stefan/7770410/working/3D/1624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020114004.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114004 none COCC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 26, 9, 9, 5, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 7, 7, 7, 19, 30, 30, 30, 30, 30, 7, 7, 1, 9, 43, 43, 43, 26, 26, 9, 9, 9, 3, 1, 1, 1, 1, 7, 19, 19, 30, 30, 1, 1, 9] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48]) total number of confs: 270 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114004 none COCC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 95, 45, 45, 24, 45, 45, 13, 13, 13, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 45, 117, 117, 117, 95, 95, 45, 45, 45, 13, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 45] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 517 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114004 none COCC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 45, 45, 45, 91, 117, 117, 117, 117, 117, 45, 45, 9, 1, 11, 11, 11, 6, 6, 1, 1, 1, 5, 9, 9, 9, 9, 45, 91, 91, 117, 117, 9, 9, 1] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 34, 48, 35, 27] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 473 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114004 none COCC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 120, 120, 68, 120, 120, 45, 45, 45, 36, 36, 36, 10, 10, 10, 4, 2, 1, 1, 1, 1, 1, 1, 10, 10, 36, 120, 201, 201, 201, 201, 201, 120, 120, 120, 45, 36, 36, 36, 36, 10, 4, 4, 2, 2, 36, 36, 120] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 933 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114004 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114004/1 /scratch/stefan/7770410/working/building/REAL300020114004 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1625) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1625 `/scratch/stefan/7770410/working/3D/1625' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020114004.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114004/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114004 none COCC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 26, 9, 9, 5, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 7, 7, 7, 19, 30, 30, 30, 30, 30, 7, 7, 1, 9, 43, 43, 43, 26, 26, 9, 9, 9, 3, 1, 1, 1, 1, 7, 19, 19, 30, 30, 1, 1, 9] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48]) total number of confs: 270 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114004 none COCC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 96, 46, 46, 24, 46, 46, 13, 13, 13, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 46, 116, 116, 116, 96, 96, 46, 46, 46, 13, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 46] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 519 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114004 none COCC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 46, 46, 46, 90, 117, 117, 117, 117, 117, 46, 46, 9, 1, 11, 11, 11, 6, 6, 1, 1, 1, 5, 9, 9, 9, 9, 46, 90, 90, 117, 117, 9, 9, 1] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 34, 48, 35, 27] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 468 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114004 none COCC1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 121, 121, 69, 121, 121, 46, 46, 46, 36, 36, 36, 10, 10, 10, 4, 2, 1, 1, 1, 1, 1, 1, 10, 10, 36, 121, 201, 201, 201, 201, 201, 121, 121, 121, 46, 36, 36, 36, 36, 10, 4, 4, 2, 2, 36, 36, 121] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 930 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114004 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114004 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114004/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114004/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114004 Building REAL300020114005 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114005' /scratch/stefan/7770410/working/building/REAL300020114005 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114005 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114005/0 /scratch/stefan/7770410/working/building/REAL300020114005 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1626) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1626 `/scratch/stefan/7770410/working/3D/1626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C12CCC(CC1)C2) `REAL300020114005.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114005 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C12CCC(CC1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 44, 113, 113, 113, 113, 113, 113, 44, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 113, 113, 113, 113, 113, 113, 113, 113, 113, 113, 113] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 249 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114005 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C12CCC(CC1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 52, 52, 52, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 52, 90, 201, 201, 201, 201, 201, 201, 90, 52, 52, 52, 52, 10, 6, 6, 4, 4, 52, 52, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 437 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114005 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C12CCC(CC1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 34, 50, 52, 52, 52, 52, 13, 13, 1, 6, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 34, 34, 50, 50, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114005 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C12CCC(CC1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 16, 16, 16, 113, 113, 113, 174, 201, 201, 201, 201, 201, 113, 113, 16, 1, 1, 1, 1, 1, 1, 1, 4, 16, 16, 16, 16, 113, 174, 174, 201, 201, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 625 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114005 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114005/1 /scratch/stefan/7770410/working/building/REAL300020114005 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1627) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1627 `/scratch/stefan/7770410/working/3D/1627' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C12CCC(CC1)C2) `REAL300020114005.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114005/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114005 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C12CCC(CC1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 45, 114, 114, 114, 114, 114, 114, 45, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 114, 114, 114, 114, 114, 114, 114, 114, 114, 114, 114] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 252 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114005 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C12CCC(CC1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 52, 52, 52, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 52, 91, 201, 201, 201, 201, 201, 201, 91, 52, 52, 52, 52, 10, 6, 6, 4, 4, 52, 52, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 438 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114005 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C12CCC(CC1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 34, 50, 52, 52, 52, 52, 13, 13, 1, 6, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 34, 34, 50, 50, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114005 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C12CCC(CC1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 16, 16, 16, 114, 114, 114, 176, 201, 201, 201, 201, 201, 114, 114, 16, 1, 1, 1, 1, 1, 1, 1, 4, 16, 16, 16, 16, 114, 176, 176, 201, 201, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 620 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114005 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114005 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114005/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114005/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114005 Building REAL300020114006 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114006' /scratch/stefan/7770410/working/building/REAL300020114006 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for REAL300020114006 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114006/0 /scratch/stefan/7770410/working/building/REAL300020114006 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1628) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1628 `/scratch/stefan/7770410/working/3D/1628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@@H+]1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114006.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114006 none C[N@@H+]1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 27, 27, 27, 27, 27, 27, 13, 13, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 13, 27, 27, 27, 27, 1, 1] 78 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 49, 50, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 146 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114006 none C[N@@H+]1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 69, 69, 69, 69, 42, 42, 42, 13, 13, 13, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 13, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 42, 13, 13, 13, 13, 1, 5, 5, 5, 5, 13, 13] 78 rigid atoms, others: [44, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 222 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114006 none C[N@@H+]1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 22, 22, 22, 69, 69, 69, 78, 78, 78, 78, 78, 78, 69, 69, 22, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 22, 22, 22, 22, 69, 78, 78, 78, 78, 22, 22] 78 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 35, 32, 36, 33, 38, 37, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114006 none C[N@@H+]1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 78, 78, 78, 78, 61, 61, 61, 27, 27, 27, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 27, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 61, 27, 27, 27, 27, 5, 3, 3, 1, 1, 27, 27] 78 rigid atoms, others: [47, 48, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50]) total number of confs: 236 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114006 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114006/1 /scratch/stefan/7770410/working/building/REAL300020114006 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1629) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1629 `/scratch/stefan/7770410/working/3D/1629' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@H+]1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114006.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114006 none C[N@H+]1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 10, 10, 10, 10, 10, 10, 9, 9, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 1, 1, 1, 9, 10, 10, 10, 10, 1, 1] 19 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 49, 50, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 32 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114006 none C[N@H+]1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 16, 16, 16, 9, 9, 9, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 16, 9, 9, 9, 9, 1, 4, 4, 4, 4, 9, 9] 19 rigid atoms, others: [44, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 63 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114006 none C[N@H+]1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 7, 7, 7, 18, 18, 18, 19, 19, 19, 19, 19, 19, 18, 18, 7, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 18, 19, 19, 19, 19, 7, 7] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 35, 32, 36, 33, 38, 37, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114006 none C[N@H+]1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 17, 17, 17, 11, 11, 11, 5, 5, 5, 4, 2, 1, 1, 1, 1, 1, 1, 5, 5, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 17, 11, 11, 11, 11, 5, 4, 4, 2, 2, 11, 11] 19 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 62 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114006 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `2' /scratch/stefan/7770410/working/building/REAL300020114006/2 /scratch/stefan/7770410/working/building/REAL300020114006 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 2 (index: 1630) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1630 `/scratch/stefan/7770410/working/3D/1630' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCCCC1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114006.mol2' -> `2.mol2' `temp.mol2' -> `REAL300020114006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114006/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114006 none CN1CCCCC1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 23, 23, 23, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 35, 50, 50, 50, 50, 50, 13, 13, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 13, 35, 35, 50, 50, 1, 1] 201 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 48, 49, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 262 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114006 none CN1CCCCC1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 131, 131, 131, 131, 60, 60, 60, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 60, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [43, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 411 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114006 none CN1CCCCC1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 23, 23, 131, 131, 131, 188, 201, 201, 201, 201, 201, 131, 131, 23, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 23, 23, 23, 23, 131, 188, 188, 201, 201, 23, 23] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 37, 35, 36, 33, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 576 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114006 none CN1CCCCC1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 151, 151, 151, 52, 52, 52, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 52, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 151, 52, 52, 52, 52, 9, 4, 4, 2, 2, 52, 52] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 611 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114006 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `3' /scratch/stefan/7770410/working/building/REAL300020114006/3 /scratch/stefan/7770410/working/building/REAL300020114006 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 3 (index: 1631) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1631 `/scratch/stefan/7770410/working/3D/1631' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114006.mol2' -> `3.mol2' `temp.mol2' -> `REAL300020114006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114006/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114006 none CN1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 23, 23, 23, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 36, 51, 51, 51, 51, 51, 13, 13, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 13, 36, 36, 51, 51, 1, 1] 201 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 48, 49, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 265 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114006 none CN1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [129, 129, 129, 129, 129, 129, 60, 60, 60, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 129, 129, 129, 129, 129, 129, 129, 129, 129, 129, 129, 129, 60, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [43, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 405 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114006 none CN1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 23, 23, 129, 129, 129, 187, 201, 201, 201, 201, 201, 129, 129, 23, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 23, 23, 23, 23, 129, 187, 187, 201, 201, 23, 23] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 37, 35, 36, 33, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 583 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114006 none CN1CCCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 150, 150, 150, 51, 51, 51, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 51, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 150, 51, 51, 51, 51, 9, 4, 4, 2, 2, 51, 51] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 611 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114006 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114006 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 2: /scratch/stefan/7770410/working/building/REAL300020114006/2.* 1: /scratch/stefan/7770410/working/building/REAL300020114006/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114006/0.* 3: /scratch/stefan/7770410/working/building/REAL300020114006/3.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114006 Building REAL300020114007 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114007' /scratch/stefan/7770410/working/building/REAL300020114007 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114007 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114007/0 /scratch/stefan/7770410/working/building/REAL300020114007 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1632) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1632 `/scratch/stefan/7770410/working/3D/1632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1Cl) `REAL300020114007.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114007 none CN1N=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 33, 48, 62, 62, 62, 62, 7, 7, 1, 25, 25, 25, 25, 25, 25, 6, 1, 1, 1, 1, 7, 33, 33, 48, 48, 1, 1] 140 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 40, 41, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) total number of confs: 258 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114007 none CN1N=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 25, 25, 25, 7, 7, 7, 1, 1, 1, 1, 1, 8, 16, 23, 23, 23, 23, 1, 1, 7, 63, 63, 63, 63, 63, 63, 25, 7, 7, 7, 7, 1, 8, 8, 16, 16, 7, 7] 140 rigid atoms, others: [35, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 197 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114007 none CN1N=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 25, 25, 63, 63, 63, 116, 140, 140, 140, 140, 140, 63, 63, 25, 1, 1, 2, 2, 2, 1, 7, 25, 25, 25, 25, 63, 116, 116, 140, 140, 25, 25] 140 rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 25, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 532 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114007 none CN1N=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [140, 140, 140, 140, 84, 84, 84, 65, 65, 65, 27, 27, 27, 9, 4, 1, 1, 1, 1, 1, 1, 27, 27, 65, 140, 140, 140, 140, 140, 140, 84, 65, 65, 65, 65, 27, 9, 9, 4, 4, 65, 65] 140 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 318 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114007 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114007/1 /scratch/stefan/7770410/working/building/REAL300020114007 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1633) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1633 `/scratch/stefan/7770410/working/3D/1633' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1Cl) `REAL300020114007.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114007/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114007 none CN1N=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 33, 48, 62, 62, 62, 62, 7, 7, 1, 25, 25, 25, 25, 25, 25, 6, 1, 1, 1, 1, 7, 33, 33, 48, 48, 1, 1] 140 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 40, 41, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) total number of confs: 258 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114007 none CN1N=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 25, 25, 25, 7, 7, 7, 1, 1, 1, 1, 1, 8, 16, 23, 23, 23, 23, 1, 1, 7, 63, 63, 63, 63, 63, 63, 25, 7, 7, 7, 7, 1, 8, 8, 16, 16, 7, 7] 140 rigid atoms, others: [35, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 197 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114007 none CN1N=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 25, 25, 63, 63, 63, 116, 140, 140, 140, 140, 140, 63, 63, 25, 1, 1, 2, 2, 2, 1, 7, 25, 25, 25, 25, 63, 116, 116, 140, 140, 25, 25] 140 rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 25, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 532 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114007 none CN1N=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [140, 140, 140, 140, 85, 85, 85, 66, 66, 66, 28, 28, 28, 9, 4, 1, 1, 1, 1, 1, 1, 28, 28, 66, 140, 140, 140, 140, 140, 140, 85, 66, 66, 66, 66, 28, 9, 9, 4, 4, 66, 66] 140 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 318 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114007 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114007 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114007/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114007/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114007 Building REAL300020114008 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114008' /scratch/stefan/7770410/working/building/REAL300020114008 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114008 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114008/0 /scratch/stefan/7770410/working/building/REAL300020114008 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1634) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1634 `/scratch/stefan/7770410/working/3D/1634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C(F)(F)F)CCC1) `REAL300020114008.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114008 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C(F)(F)F)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 15, 15, 15, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 43, 88, 88, 88, 88, 88, 88, 88, 43, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 88, 88, 88, 88, 88, 88] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 304 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114008 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C(F)(F)F)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 15, 15, 15, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [180, 180, 67, 67, 67, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 67, 180, 201, 201, 201, 201, 201, 201, 201, 180, 67, 67, 67, 67, 11, 6, 6, 4, 4, 67, 67, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 571 number of broken/clashed sets: 14 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114008 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C(F)(F)F)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 15, 15, 15, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 41, 58, 67, 67, 67, 67, 11, 11, 1, 6, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 11, 41, 41, 58, 58, 1, 1, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 288 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114008 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C(F)(F)F)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 15, 15, 15, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 13, 13, 13, 88, 88, 88, 167, 201, 201, 201, 201, 201, 88, 88, 13, 1, 1, 2, 2, 2, 1, 1, 1, 4, 13, 13, 13, 13, 88, 167, 167, 201, 201, 13, 13, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 39, 40, 41, 42, 43, 44, 19, 20, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 747 number of broken/clashed sets: 14 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114008 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114008/1 /scratch/stefan/7770410/working/building/REAL300020114008 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1635) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1635 `/scratch/stefan/7770410/working/3D/1635' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C(F)(F)F)CCC1) `REAL300020114008.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114008 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C(F)(F)F)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 15, 15, 15, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 43, 88, 88, 88, 88, 88, 88, 88, 43, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 88, 88, 88, 88, 88, 88] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 304 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114008 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C(F)(F)F)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 15, 15, 15, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [180, 180, 67, 67, 67, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 67, 180, 201, 201, 201, 201, 201, 201, 201, 180, 67, 67, 67, 67, 11, 6, 6, 4, 4, 67, 67, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 571 number of broken/clashed sets: 14 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114008 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C(F)(F)F)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 15, 15, 15, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 41, 58, 67, 67, 67, 67, 11, 11, 1, 6, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 11, 41, 41, 58, 58, 1, 1, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 288 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114008 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C(F)(F)F)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 15, 15, 15, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 13, 13, 13, 88, 88, 88, 167, 201, 201, 201, 201, 201, 88, 88, 13, 1, 1, 2, 2, 2, 1, 1, 1, 4, 13, 13, 13, 13, 88, 167, 167, 201, 201, 13, 13, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 39, 40, 41, 42, 43, 44, 19, 20, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 747 number of broken/clashed sets: 14 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114008 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114008 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114008/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114008/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114008 Building REAL300020114009 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114009' /scratch/stefan/7770410/working/building/REAL300020114009 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114009 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114009/0 /scratch/stefan/7770410/working/building/REAL300020114009 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1636) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1636 `/scratch/stefan/7770410/working/3D/1636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC=C(F)C=C1F) `REAL300020114009.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114009 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC=C(F)C=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 15, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1, 5, 11, 22, 22, 22, 22, 22, 22, 22, 11, 5, 5, 5, 5, 1, 7, 7, 7, 7, 5, 5, 22, 22] 29 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114009 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC=C(F)C=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 15, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 8, 8, 8, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 8, 16, 29, 29, 29, 29, 29, 29, 29, 16, 8, 8, 8, 8, 7, 4, 4, 2, 2, 8, 8, 29, 29] 29 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 67 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114009 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC=C(F)C=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 15, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 8, 5, 5, 1, 6, 19, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 5, 8, 8, 8, 8, 1, 1, 20, 20] 29 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114009 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC=C(F)C=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 15, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 20, 20, 20, 22, 22, 22, 29, 29, 29, 29, 29, 29, 22, 22, 20, 1, 1, 1, 1, 1, 1, 1, 1, 11, 20, 20, 20, 20, 22, 29, 29, 29, 29, 20, 20, 1, 1] 29 rigid atoms, others: [1, 39, 40, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 97 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114009 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114009/1 /scratch/stefan/7770410/working/building/REAL300020114009 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1637) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1637 `/scratch/stefan/7770410/working/3D/1637' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC=C(F)C=C1F) `REAL300020114009.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114009 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC=C(F)C=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 15, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1, 5, 12, 23, 23, 23, 23, 23, 23, 23, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 5, 5, 23, 23] 30 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 67 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114009 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC=C(F)C=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 15, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 8, 8, 8, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 8, 17, 30, 30, 30, 30, 30, 30, 30, 17, 8, 8, 8, 8, 7, 4, 4, 2, 2, 8, 8, 30, 30] 30 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 71 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114009 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC=C(F)C=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 15, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 8, 5, 5, 1, 6, 20, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 5, 8, 8, 8, 8, 1, 1, 21, 21] 30 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114009 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC=C(F)C=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 15, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 21, 21, 21, 23, 23, 23, 30, 30, 30, 30, 30, 30, 23, 23, 21, 1, 1, 1, 1, 1, 1, 1, 1, 11, 21, 21, 21, 21, 23, 30, 30, 30, 30, 21, 21, 1, 1] 30 rigid atoms, others: [1, 39, 40, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 99 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114009 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114009 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114009/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114009/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114009 Building REAL300020114010 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114010' /scratch/stefan/7770410/working/building/REAL300020114010 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114010 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114010/0 /scratch/stefan/7770410/working/building/REAL300020114010 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1638) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1638 `/scratch/stefan/7770410/working/3D/1638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)S(C)(=O)=O) `REAL300020114010.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114010 none CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 5, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 44, 44, 44, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 11, 89, 97, 97, 97, 89, 89, 89, 89, 44, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 97, 97, 97] 201 rigid atoms, others: [34, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 412 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114010 none CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 5, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 133, 133, 133, 63, 63, 63, 14, 14, 14, 7, 4, 1, 1, 1, 1, 1, 1, 14, 14, 63, 201, 201, 201, 201, 201, 201, 201, 201, 133, 63, 63, 63, 63, 14, 7, 7, 4, 4, 63, 63, 201, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 750 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114010 none CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 5, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 41, 58, 68, 68, 68, 68, 11, 11, 1, 22, 28, 28, 28, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 41, 41, 58, 58, 1, 1, 28, 28, 28] 201 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 39, 40, 20, 30, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43]) total number of confs: 365 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114010 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114010/1 /scratch/stefan/7770410/working/building/REAL300020114010 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1639) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1639 `/scratch/stefan/7770410/working/3D/1639' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)S(C)(=O)=O) `REAL300020114010.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114010/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114010 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 5, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 44, 44, 44, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 11, 89, 96, 96, 96, 89, 89, 89, 89, 44, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 96, 96, 96] 201 rigid atoms, others: [34, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 406 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114010 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 5, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 131, 131, 131, 61, 61, 61, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 61, 201, 201, 201, 201, 201, 201, 201, 201, 131, 61, 61, 61, 61, 12, 6, 6, 4, 4, 61, 61, 201, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 755 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114010 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 5, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 41, 58, 68, 68, 68, 68, 11, 11, 1, 22, 28, 28, 28, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 41, 41, 58, 58, 1, 1, 28, 28, 28] 201 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 39, 40, 20, 30, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43]) total number of confs: 365 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114010 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114010 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114010/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114010/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114010 Building REAL300020114011 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114011' /scratch/stefan/7770410/working/building/REAL300020114011 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114011 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114011/0 /scratch/stefan/7770410/working/building/REAL300020114011 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1640) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1640 `/scratch/stefan/7770410/working/3D/1640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114011.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114011 none CS(=O)(=O)CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [123, 117, 123, 123, 96, 23, 23, 23, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 11, 11, 11, 11, 1, 1, 9, 123, 123, 123, 117, 117, 96, 96, 23, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 535 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114011 none CS(=O)(=O)CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 26, 17, 17, 17, 17, 17, 17, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 8, 8, 17, 33, 33, 33, 33, 33, 26, 26, 17, 17, 17, 17, 17, 8, 4, 4, 4, 4, 17, 17] 33 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 137 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114011 none CS(=O)(=O)CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 39, 44, 44, 29, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 31, 40, 50, 50, 50, 50, 9, 9, 1, 44, 44, 44, 39, 39, 29, 29, 6, 1, 1, 1, 1, 9, 31, 31, 40, 40, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 354 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114011 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114011/1 /scratch/stefan/7770410/working/building/REAL300020114011 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1641) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1641 `/scratch/stefan/7770410/working/3D/1641' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114011.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114011 none CS(=O)(=O)CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 118, 124, 124, 96, 23, 23, 23, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 11, 11, 11, 11, 1, 1, 9, 124, 124, 124, 118, 118, 96, 96, 23, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 541 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114011 none CS(=O)(=O)CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 26, 16, 16, 16, 16, 16, 16, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 7, 7, 16, 33, 33, 33, 33, 33, 26, 26, 16, 16, 16, 16, 16, 7, 4, 4, 4, 4, 16, 16] 33 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 139 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114011 none CS(=O)(=O)CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 39, 44, 44, 29, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 32, 41, 51, 51, 51, 51, 9, 9, 1, 44, 44, 44, 39, 39, 29, 29, 6, 1, 1, 1, 1, 9, 32, 32, 41, 41, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 357 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114011 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114011 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114011/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114011/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114011 Building REAL300020114012 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114012' /scratch/stefan/7770410/working/building/REAL300020114012 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114012 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114012/0 /scratch/stefan/7770410/working/building/REAL300020114012 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1642) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1642 `/scratch/stefan/7770410/working/3D/1642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114012.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114012 none COCCS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [137, 119, 119, 100, 76, 100, 100, 23, 23, 23, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 137, 137, 137, 119, 119, 119, 119, 76, 76, 23, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 595 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114012 none COCCS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 197, 136, 110, 136, 136, 52, 52, 52, 34, 34, 34, 8, 8, 8, 5, 2, 1, 1, 1, 1, 1, 1, 8, 8, 34, 201, 201, 201, 201, 201, 197, 197, 110, 110, 52, 34, 34, 34, 34, 8, 5, 5, 2, 2, 34, 34] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 952 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114012 none COCCS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 42, 42, 26, 20, 26, 26, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 35, 35, 35, 35, 8, 8, 1, 63, 63, 63, 42, 42, 42, 42, 20, 20, 5, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 370 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114012 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114012/1 /scratch/stefan/7770410/working/building/REAL300020114012 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1643) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1643 `/scratch/stefan/7770410/working/3D/1643' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114012.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114012 none COCCS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 117, 117, 101, 76, 101, 101, 23, 23, 23, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 133, 133, 133, 117, 117, 117, 117, 76, 76, 23, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 580 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114012 none COCCS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 197, 136, 110, 136, 136, 51, 51, 51, 33, 33, 33, 8, 8, 8, 5, 2, 1, 1, 1, 1, 1, 1, 8, 8, 33, 201, 201, 201, 201, 201, 197, 197, 110, 110, 51, 33, 33, 33, 33, 8, 5, 5, 2, 2, 33, 33] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 953 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114012 none COCCS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 42, 42, 27, 20, 27, 27, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 35, 35, 35, 35, 8, 8, 1, 60, 60, 60, 42, 42, 42, 42, 20, 20, 5, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 368 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114012 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114012 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114012/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114012/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114012 Building REAL300020114013 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114013' /scratch/stefan/7770410/working/building/REAL300020114013 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114013 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114013/0 /scratch/stefan/7770410/working/building/REAL300020114013 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1644) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1644 `/scratch/stefan/7770410/working/3D/1644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114013.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114013 none CC(C)CS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 105, 89, 105, 105, 32, 32, 32, 10, 10, 10, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 10, 105, 105, 105, 105, 105, 105, 105, 105, 105, 89, 89, 32, 10, 10, 10, 10, 1, 7, 7, 9, 9, 10, 10] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 448 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114013 none CC(C)CS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 110, 110, 110, 51, 51, 51, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 51, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 110, 51, 51, 51, 51, 11, 6, 6, 4, 4, 51, 51] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 723 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114013 none CC(C)CS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 24, 32, 32, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 33, 47, 50, 50, 50, 50, 10, 10, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 24, 24, 6, 1, 1, 1, 1, 10, 33, 33, 47, 47, 1, 1] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 323 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114013 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114013/1 /scratch/stefan/7770410/working/building/REAL300020114013 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1645) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1645 `/scratch/stefan/7770410/working/3D/1645' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114013.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114013/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114013 none CC(C)CS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 105, 90, 105, 105, 32, 32, 32, 10, 10, 10, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 10, 105, 105, 105, 105, 105, 105, 105, 105, 105, 90, 90, 32, 10, 10, 10, 10, 1, 7, 7, 9, 9, 10, 10] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 445 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114013 none CC(C)CS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 109, 109, 109, 51, 51, 51, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 51, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 109, 51, 51, 51, 51, 11, 6, 6, 4, 4, 51, 51] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 725 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114013 none CC(C)CS(=O)(=O)CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 24, 32, 32, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 33, 47, 50, 50, 50, 50, 10, 10, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 24, 24, 6, 1, 1, 1, 1, 10, 33, 33, 47, 47, 1, 1] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 323 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114013 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114013 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114013/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114013/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114013 Building REAL300020114014 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114014' /scratch/stefan/7770410/working/building/REAL300020114014 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114014 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114014/0 /scratch/stefan/7770410/working/building/REAL300020114014 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1646) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1646 `/scratch/stefan/7770410/working/3D/1646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CN2C=CC=CC2=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114014.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114014 none O=C(CC1=CN2C=CC=CC2=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 27, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 9, 9, 9, 32, 44, 45, 45, 45, 45, 9, 9, 1, 27, 27, 35, 35, 35, 35, 35, 6, 1, 1, 1, 1, 9, 32, 32, 44, 44, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 46, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 280 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114014 none O=C(CC1=CN2C=CC=CC2=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 98, 111, 111, 111, 111, 111, 111, 111, 111, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 10, 10, 10, 10, 1, 1, 9, 98, 98, 111, 111, 111, 111, 111, 30, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 400 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114014 none O=C(CC1=CN2C=CC=CC2=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 35, 35, 35, 111, 111, 111, 174, 201, 201, 201, 201, 201, 111, 111, 35, 7, 7, 1, 1, 1, 1, 1, 15, 35, 35, 35, 35, 111, 174, 174, 201, 201, 35, 35] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 684 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114014 none O=C(CC1=CN2C=CC=CC2=N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 193, 201, 201, 201, 201, 201, 201, 201, 201, 45, 45, 45, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 45, 193, 193, 201, 201, 201, 201, 201, 91, 45, 45, 45, 45, 10, 5, 5, 3, 3, 45, 45] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 739 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114014 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114014/1 /scratch/stefan/7770410/working/building/REAL300020114014 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1647) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1647 `/scratch/stefan/7770410/working/3D/1647' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CN2C=CC=CC2=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114014.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114014/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114014 none O=C(CC1=CN2C=CC=CC2=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 27, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 9, 9, 9, 33, 45, 46, 46, 46, 46, 9, 9, 1, 27, 27, 35, 35, 35, 35, 35, 6, 1, 1, 1, 1, 9, 33, 33, 45, 45, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 46, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 283 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114014 none O=C(CC1=CN2C=CC=CC2=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 98, 111, 111, 111, 111, 111, 111, 111, 111, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 10, 10, 10, 10, 1, 1, 9, 98, 98, 111, 111, 111, 111, 111, 30, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 400 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114014 none O=C(CC1=CN2C=CC=CC2=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 35, 35, 35, 111, 111, 111, 174, 201, 201, 201, 201, 201, 111, 111, 35, 7, 7, 1, 1, 1, 1, 1, 15, 35, 35, 35, 35, 111, 174, 174, 201, 201, 35, 35] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 681 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114014 none O=C(CC1=CN2C=CC=CC2=N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 193, 201, 201, 201, 201, 201, 201, 201, 201, 45, 45, 45, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 45, 193, 193, 201, 201, 201, 201, 201, 92, 45, 45, 45, 45, 10, 5, 5, 3, 3, 45, 45] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 737 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114014 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114014 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114014/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114014/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114014 Building REAL300020114015 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114015' /scratch/stefan/7770410/working/building/REAL300020114015 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114015 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114015/0 /scratch/stefan/7770410/working/building/REAL300020114015 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1648) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1648 `/scratch/stefan/7770410/working/3D/1648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=CN=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114015.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114015 none O=C(CC1=CC=CN=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 12, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 8, 8, 8, 21, 31, 31, 31, 31, 31, 8, 8, 1, 12, 12, 26, 26, 26, 26, 5, 1, 1, 1, 1, 8, 21, 21, 31, 31, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 190 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114015 none O=C(CC1=CC=CN=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 53, 101, 101, 101, 101, 101, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 53, 53, 101, 101, 101, 101, 17, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [37, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 314 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114015 none O=C(CC1=CC=CN=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 1, 1, 1, 1, 1, 1, 1, 13, 13, 26, 26, 26, 101, 101, 101, 161, 201, 201, 201, 201, 201, 101, 101, 26, 7, 7, 1, 1, 1, 1, 13, 26, 26, 26, 26, 101, 161, 161, 201, 201, 26, 26] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 735 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114015 none O=C(CC1=CC=CN=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 114, 201, 201, 201, 201, 201, 31, 31, 31, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 31, 114, 114, 201, 201, 201, 201, 45, 31, 31, 31, 31, 7, 4, 4, 2, 2, 31, 31] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 613 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114015 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114015/1 /scratch/stefan/7770410/working/building/REAL300020114015 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1649) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1649 `/scratch/stefan/7770410/working/3D/1649' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=CN=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114015.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114015/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114015 none O=C(CC1=CC=CN=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 12, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 8, 8, 8, 21, 31, 31, 31, 31, 31, 8, 8, 1, 12, 12, 26, 26, 26, 26, 5, 1, 1, 1, 1, 8, 21, 21, 31, 31, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 190 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114015 none O=C(CC1=CC=CN=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 53, 101, 101, 101, 101, 101, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 53, 53, 101, 101, 101, 101, 17, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [37, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 314 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114015 none O=C(CC1=CC=CN=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 1, 1, 1, 1, 1, 1, 1, 13, 13, 26, 26, 26, 101, 101, 101, 162, 201, 201, 201, 201, 201, 101, 101, 26, 7, 7, 1, 1, 1, 1, 13, 26, 26, 26, 26, 101, 162, 162, 201, 201, 26, 26] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 735 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114015 none O=C(CC1=CC=CN=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 115, 201, 201, 201, 201, 201, 31, 31, 31, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 31, 115, 115, 201, 201, 201, 201, 46, 31, 31, 31, 31, 7, 4, 4, 2, 2, 31, 31] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 615 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114015 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114015 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114015/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114015/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114015 Building REAL300020114016 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114016' /scratch/stefan/7770410/working/building/REAL300020114016 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114016 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114016/0 /scratch/stefan/7770410/working/building/REAL300020114016 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1650) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1650 `/scratch/stefan/7770410/working/3D/1650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1) `REAL300020114016.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114016 none CCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 10, 10, 10, 10, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 42, 60, 73, 73, 73, 73, 13, 13, 1, 10, 24, 24, 24, 24, 24, 10, 10, 6, 1, 1, 1, 1, 13, 42, 42, 60, 60, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 347 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114016 none CCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 54, 54, 54, 54, 48, 48, 48, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 11, 11, 11, 11, 1, 1, 13, 54, 108, 108, 108, 108, 108, 54, 54, 48, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 454 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114016 none CCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 54, 54, 54, 119, 149, 159, 159, 159, 159, 54, 54, 10, 1, 6, 6, 6, 6, 6, 1, 1, 4, 10, 10, 10, 10, 54, 119, 119, 149, 149, 10, 10] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 25, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 588 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114016 none CCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 157, 157, 157, 157, 157, 157, 157, 74, 74, 74, 12, 12, 12, 7, 4, 1, 1, 1, 1, 1, 1, 12, 12, 74, 157, 201, 201, 201, 201, 201, 157, 157, 157, 74, 74, 74, 74, 12, 7, 7, 4, 4, 74, 74] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 711 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114016 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114016/1 /scratch/stefan/7770410/working/building/REAL300020114016 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1651) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1651 `/scratch/stefan/7770410/working/3D/1651' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1) `REAL300020114016.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114016 none CCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 10, 10, 10, 10, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 42, 60, 73, 73, 73, 73, 13, 13, 1, 10, 24, 24, 24, 24, 24, 10, 10, 6, 1, 1, 1, 1, 13, 42, 42, 60, 60, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 347 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114016 none CCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 54, 54, 54, 54, 48, 48, 48, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 11, 11, 11, 11, 1, 1, 13, 54, 107, 107, 107, 107, 107, 54, 54, 48, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 451 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114016 none CCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 54, 54, 54, 119, 150, 159, 159, 159, 159, 54, 54, 10, 1, 6, 6, 6, 6, 6, 1, 1, 4, 10, 10, 10, 10, 54, 119, 119, 150, 150, 10, 10] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 25, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 592 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114016 none CCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 158, 158, 158, 158, 158, 158, 158, 74, 74, 74, 12, 12, 12, 7, 4, 1, 1, 1, 1, 1, 1, 12, 12, 74, 158, 201, 201, 201, 201, 201, 158, 158, 158, 74, 74, 74, 74, 12, 7, 7, 4, 4, 74, 74] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 713 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114016 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114016 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114016/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114016/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114016 Building REAL300020114017 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114017' /scratch/stefan/7770410/working/building/REAL300020114017 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114017 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114017/0 /scratch/stefan/7770410/working/building/REAL300020114017 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1652) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1652 `/scratch/stefan/7770410/working/3D/1652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020114017.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114017 none NC(=O)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 15, 19, 15, 15, 15, 15, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 30, 45, 46, 46, 46, 46, 11, 11, 1, 15, 19, 19, 15, 15, 15, 5, 1, 1, 1, 1, 11, 30, 30, 45, 45, 1, 1, 15] 201 rigid atoms, others: [34, 35, 36, 37, 44, 10, 11, 12, 13, 14, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45]) total number of confs: 222 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114017 none NC(=O)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 70, 92, 70, 70, 70, 70, 25, 25, 25, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 70, 92, 92, 70, 70, 70, 25, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 70] 201 rigid atoms, others: [38, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 253 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114017 none NC(=O)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 70, 70, 70, 132, 180, 180, 180, 180, 180, 70, 70, 15, 1, 3, 3, 1, 1, 1, 5, 15, 15, 15, 15, 70, 132, 132, 180, 180, 15, 15, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 45, 27, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 715 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114017 none NC(=O)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 180, 201, 180, 180, 180, 180, 71, 71, 71, 46, 46, 46, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 46, 180, 201, 201, 180, 180, 180, 71, 46, 46, 46, 46, 9, 5, 5, 3, 3, 46, 46, 180] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 457 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114017 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114017/1 /scratch/stefan/7770410/working/building/REAL300020114017 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1653) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1653 `/scratch/stefan/7770410/working/3D/1653' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020114017.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114017/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114017 none NC(=O)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 16, 20, 16, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 30, 45, 46, 46, 46, 46, 11, 11, 1, 16, 20, 20, 16, 16, 16, 6, 1, 1, 1, 1, 11, 30, 30, 45, 45, 1, 1, 16] 201 rigid atoms, others: [34, 35, 36, 37, 44, 10, 11, 12, 13, 14, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45]) total number of confs: 224 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114017 none NC(=O)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 71, 93, 71, 71, 71, 71, 26, 26, 26, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 71, 93, 93, 71, 71, 71, 26, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 71] 201 rigid atoms, others: [38, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 255 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114017 none NC(=O)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 71, 71, 71, 133, 181, 181, 181, 181, 181, 71, 71, 16, 1, 3, 3, 1, 1, 1, 5, 16, 16, 16, 16, 71, 133, 133, 181, 181, 16, 16, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 45, 27, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 717 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114017 none NC(=O)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 181, 201, 181, 181, 181, 181, 72, 72, 72, 46, 46, 46, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 46, 181, 201, 201, 181, 181, 181, 72, 46, 46, 46, 46, 9, 5, 5, 3, 3, 46, 46, 181] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 457 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114017 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114017 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114017/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114017/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114017 Building REAL300020114018 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114018' /scratch/stefan/7770410/working/building/REAL300020114018 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114018 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114018/0 /scratch/stefan/7770410/working/building/REAL300020114018 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1654) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1654 `/scratch/stefan/7770410/working/3D/1654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1=O) `REAL300020114018.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114018 none CN1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 29, 43, 48, 48, 48, 48, 11, 11, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 29, 29, 43, 43, 1, 1, 22, 22] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 45, 46, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 238 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114018 none CN1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 102, 32, 32, 32, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 32, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 102, 102] 201 rigid atoms, others: [40, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 299 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114018 none CN1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 22, 22, 22, 102, 102, 102, 156, 201, 201, 201, 201, 201, 102, 102, 22, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 8, 22, 22, 22, 22, 102, 156, 156, 201, 201, 22, 22, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 47, 48, 24, 25, 26, 5, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 728 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114018 none CN1CCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 96, 96, 96, 50, 50, 50, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 50, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 96, 50, 50, 50, 50, 11, 6, 6, 4, 4, 50, 50, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 591 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114018 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114018/1 /scratch/stefan/7770410/working/building/REAL300020114018 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1655) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1655 `/scratch/stefan/7770410/working/3D/1655' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1=O) `REAL300020114018.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114018 none CN1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 29, 43, 48, 48, 48, 48, 11, 11, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 29, 29, 43, 43, 1, 1, 22, 22] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 45, 46, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 238 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114018 none CN1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 102, 32, 32, 32, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 32, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 102, 102] 201 rigid atoms, others: [40, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 299 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114018 none CN1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 22, 22, 22, 102, 102, 102, 156, 201, 201, 201, 201, 201, 102, 102, 22, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 8, 22, 22, 22, 22, 102, 156, 156, 201, 201, 22, 22, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 47, 48, 24, 25, 26, 5, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 728 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114018 none CN1CCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 95, 95, 95, 50, 50, 50, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 50, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 95, 50, 50, 50, 50, 11, 6, 6, 4, 4, 50, 50, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 591 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114018 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114018 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114018/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114018/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114018 Building REAL300020114019 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114019' /scratch/stefan/7770410/working/building/REAL300020114019 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114019 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114019/0 /scratch/stefan/7770410/working/building/REAL300020114019 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1656) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1656 `/scratch/stefan/7770410/working/3D/1656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1) `REAL300020114019.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114019 none C=CCOC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 32, 27, 5, 5, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 23, 34, 34, 34, 34, 34, 7, 7, 1, 13, 13, 60, 60, 60, 32, 32, 13, 13, 5, 1, 1, 1, 1, 7, 23, 23, 34, 34, 1, 1, 13, 13] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49]) total number of confs: 323 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114019 none C=CCOC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 100, 94, 21, 21, 57, 57, 21, 21, 21, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 57, 57, 119, 119, 119, 100, 100, 57, 57, 21, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7, 57, 57] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 394 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114019 none C=CCOC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 5, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 57, 57, 57, 98, 131, 131, 131, 131, 131, 57, 57, 13, 1, 1, 25, 25, 25, 5, 5, 1, 1, 5, 13, 13, 13, 13, 57, 98, 98, 131, 131, 13, 13, 1, 1] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 48, 49, 35, 27, 28] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 544 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114019 none C=CCOC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 121, 33, 33, 77, 77, 33, 33, 33, 25, 25, 25, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 25, 77, 77, 201, 201, 201, 201, 201, 77, 77, 33, 25, 25, 25, 25, 7, 4, 4, 2, 2, 25, 25, 77, 77] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 824 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114019 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114019/1 /scratch/stefan/7770410/working/building/REAL300020114019 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1657) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1657 `/scratch/stefan/7770410/working/3D/1657' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1) `REAL300020114019.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114019 none C=CCOC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 33, 27, 5, 5, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 23, 34, 34, 34, 34, 34, 7, 7, 1, 14, 14, 60, 60, 60, 33, 33, 14, 14, 5, 1, 1, 1, 1, 7, 23, 23, 34, 34, 1, 1, 14, 14] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49]) total number of confs: 330 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114019 none C=CCOC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 99, 94, 21, 21, 58, 58, 21, 21, 21, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 58, 58, 118, 118, 118, 99, 99, 58, 58, 21, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7, 58, 58] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 393 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114019 none C=CCOC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 5, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 58, 58, 58, 99, 133, 133, 133, 133, 133, 58, 58, 14, 1, 1, 25, 25, 25, 5, 5, 1, 1, 5, 14, 14, 14, 14, 58, 99, 99, 133, 133, 14, 14, 1, 1] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 48, 49, 35, 27, 28] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 552 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114019 none C=CCOC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 121, 33, 33, 77, 77, 33, 33, 33, 25, 25, 25, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 25, 77, 77, 201, 201, 201, 201, 201, 77, 77, 33, 25, 25, 25, 25, 7, 4, 4, 2, 2, 25, 25, 77, 77] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 824 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114019 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114019 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114019/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114019/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114019 Building REAL300020114020 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114020' /scratch/stefan/7770410/working/building/REAL300020114020 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114020 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114020/0 /scratch/stefan/7770410/working/building/REAL300020114020 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1658) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1658 `/scratch/stefan/7770410/working/3D/1658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114020.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114020 none C=CCOC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 49, 24, 13, 13, 13, 5, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 20, 31, 31, 31, 31, 31, 7, 7, 1, 69, 69, 69, 49, 49, 13, 13, 13, 13, 5, 1, 1, 1, 1, 7, 20, 20, 31, 31, 1, 1] 201 rigid atoms, others: [48, 39, 40, 41, 42, 12, 13, 14, 15, 16, 49, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 362 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114020 none C=CCOC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [145, 129, 82, 45, 45, 45, 20, 45, 45, 19, 19, 19, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 145, 145, 145, 129, 129, 45, 45, 45, 45, 19, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [43, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 558 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114020 none C=CCOC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 26, 8, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 45, 45, 45, 85, 120, 120, 120, 120, 120, 45, 45, 13, 38, 38, 38, 26, 26, 1, 1, 1, 1, 4, 13, 13, 13, 13, 45, 85, 85, 120, 120, 13, 13] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 10, 35, 36, 37] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 579 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114020 none C=CCOC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 116, 94, 94, 94, 49, 94, 94, 46, 46, 46, 31, 31, 31, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 31, 201, 201, 201, 201, 201, 94, 94, 94, 94, 46, 31, 31, 31, 31, 8, 4, 4, 2, 2, 31, 31] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 840 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114020 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114020/1 /scratch/stefan/7770410/working/building/REAL300020114020 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1659) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1659 `/scratch/stefan/7770410/working/3D/1659' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114020.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114020 none C=CCOC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 49, 24, 13, 13, 13, 5, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 20, 31, 31, 31, 31, 31, 7, 7, 1, 69, 69, 69, 49, 49, 13, 13, 13, 13, 5, 1, 1, 1, 1, 7, 20, 20, 31, 31, 1, 1] 201 rigid atoms, others: [48, 39, 40, 41, 42, 12, 13, 14, 15, 16, 49, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 362 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114020 none C=CCOC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [145, 129, 81, 45, 45, 45, 20, 45, 45, 19, 19, 19, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 145, 145, 145, 129, 129, 45, 45, 45, 45, 19, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [43, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 559 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114020 none C=CCOC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 26, 8, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 45, 45, 45, 85, 119, 119, 119, 119, 119, 45, 45, 13, 38, 38, 38, 26, 26, 1, 1, 1, 1, 4, 13, 13, 13, 13, 45, 85, 85, 119, 119, 13, 13] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 10, 35, 36, 37] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 573 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114020 none C=CCOC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 116, 94, 94, 94, 49, 94, 94, 46, 46, 46, 31, 31, 31, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 31, 201, 201, 201, 201, 201, 94, 94, 94, 94, 46, 31, 31, 31, 31, 9, 4, 4, 2, 2, 31, 31] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 840 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114020 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114020 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114020/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114020/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114020 Building REAL300020114021 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114021' /scratch/stefan/7770410/working/building/REAL300020114021 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114021 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114021/0 /scratch/stefan/7770410/working/building/REAL300020114021 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1660) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1660 `/scratch/stefan/7770410/working/3D/1660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC1=O) `REAL300020114021.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114021 none CN1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 34, 50, 50, 50, 50, 50, 12, 12, 1, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 12, 34, 34, 50, 50, 1, 1, 19] 201 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 235 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114021 none CN1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [121, 121, 121, 121, 45, 45, 45, 12, 12, 12, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 12, 121, 121, 121, 121, 121, 121, 121, 121, 45, 12, 12, 12, 12, 1, 6, 6, 8, 8, 12, 12, 121] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 249 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114021 none CN1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 19, 121, 121, 121, 179, 201, 201, 201, 201, 201, 121, 121, 19, 1, 1, 1, 2, 2, 2, 1, 1, 5, 19, 19, 19, 19, 121, 179, 179, 201, 201, 19, 19, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 620 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114021 none CN1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 118, 118, 118, 50, 50, 50, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 50, 201, 201, 201, 201, 201, 201, 201, 201, 118, 50, 50, 50, 50, 8, 4, 4, 2, 2, 50, 50, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 464 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114021 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114021/1 /scratch/stefan/7770410/working/building/REAL300020114021 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1661) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1661 `/scratch/stefan/7770410/working/3D/1661' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC1=O) `REAL300020114021.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114021 none CN1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 34, 50, 50, 50, 50, 50, 12, 12, 1, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 12, 34, 34, 50, 50, 1, 1, 19] 201 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 235 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114021 none CN1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [121, 121, 121, 121, 45, 45, 45, 12, 12, 12, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 12, 121, 121, 121, 121, 121, 121, 121, 121, 45, 12, 12, 12, 12, 1, 6, 6, 8, 8, 12, 12, 121] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 250 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114021 none CN1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 19, 121, 121, 121, 179, 201, 201, 201, 201, 201, 121, 121, 19, 1, 1, 1, 2, 2, 2, 1, 1, 5, 19, 19, 19, 19, 121, 179, 179, 201, 201, 19, 19, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 620 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114021 none CN1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 119, 119, 119, 50, 50, 50, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 50, 201, 201, 201, 201, 201, 201, 201, 201, 119, 50, 50, 50, 50, 8, 4, 4, 2, 2, 50, 50, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 467 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114021 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114021 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114021/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114021/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114021 Building REAL300020114022 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114022' /scratch/stefan/7770410/working/building/REAL300020114022 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114022 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114022/0 /scratch/stefan/7770410/working/building/REAL300020114022 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1662) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1662 `/scratch/stefan/7770410/working/3D/1662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)NCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114022.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114022 none CC(=O)NCC(=O)NCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [161, 161, 161, 153, 82, 82, 82, 68, 17, 17, 17, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 161, 161, 161, 161, 153, 153, 82, 68, 68, 17, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 679 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114022 none CC(=O)NCC(=O)NCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 180, 98, 98, 98, 87, 42, 42, 42, 30, 30, 30, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 30, 201, 201, 201, 201, 180, 180, 98, 87, 87, 42, 30, 30, 30, 30, 8, 4, 4, 2, 2, 30, 30] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 812 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114022 none CC(=O)NCC(=O)NCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 88, 27, 27, 27, 20, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 18, 30, 30, 30, 30, 30, 7, 7, 1, 101, 101, 101, 101, 88, 88, 27, 20, 20, 5, 1, 1, 1, 1, 7, 18, 18, 30, 30, 1, 1] 201 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 511 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114022 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114022/1 /scratch/stefan/7770410/working/building/REAL300020114022 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1663) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1663 `/scratch/stefan/7770410/working/3D/1663' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)NCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114022.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114022 none CC(=O)NCC(=O)NCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 162, 154, 82, 82, 82, 68, 17, 17, 17, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 162, 162, 162, 162, 154, 154, 82, 68, 68, 17, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 688 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114022 none CC(=O)NCC(=O)NCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 180, 98, 98, 98, 87, 42, 42, 42, 30, 30, 30, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 30, 201, 201, 201, 201, 180, 180, 98, 87, 87, 42, 30, 30, 30, 30, 8, 4, 4, 2, 2, 30, 30] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 812 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114022 none CC(=O)NCC(=O)NCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 89, 27, 27, 27, 20, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 18, 30, 30, 30, 30, 30, 7, 7, 1, 102, 102, 102, 102, 89, 89, 27, 20, 20, 5, 1, 1, 1, 1, 7, 18, 18, 30, 30, 1, 1] 201 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 514 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114022 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114022 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114022/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114022/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114022 Building REAL300020114023 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114023' /scratch/stefan/7770410/working/building/REAL300020114023 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114023 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114023/0 /scratch/stefan/7770410/working/building/REAL300020114023 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1664) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1664 `/scratch/stefan/7770410/working/3D/1664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(F)(F)CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114023.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114023 none CC(F)(F)CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 15, 15, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 119, 125, 125, 96, 23, 23, 23, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 11, 11, 11, 11, 1, 1, 9, 125, 125, 125, 119, 119, 96, 96, 23, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 550 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114023 none CC(F)(F)CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 15, 15, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 22, 39, 39, 15, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 39, 39, 39, 22, 22, 15, 15, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 6, 6] 39 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 185 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114023 none CC(F)(F)CCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 15, 15, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 41, 49, 49, 30, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 35, 42, 54, 54, 54, 54, 9, 9, 1, 49, 49, 49, 41, 41, 30, 30, 5, 1, 1, 1, 1, 9, 35, 35, 42, 42, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 389 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114023 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114023/1 /scratch/stefan/7770410/working/building/REAL300020114023 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1665) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1665 `/scratch/stefan/7770410/working/3D/1665' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(F)(F)CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114023.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114023/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114023 none CC(F)(F)CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 15, 15, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 119, 125, 125, 95, 23, 23, 23, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 11, 11, 11, 11, 1, 1, 9, 125, 125, 125, 119, 119, 95, 95, 23, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 553 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114023 none CC(F)(F)CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 15, 15, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 21, 39, 39, 14, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 39, 39, 39, 21, 21, 14, 14, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 6, 6] 39 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 185 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114023 none CC(F)(F)CCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 15, 15, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 41, 49, 49, 30, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 35, 42, 54, 54, 54, 54, 9, 9, 1, 49, 49, 49, 41, 41, 30, 30, 5, 1, 1, 1, 1, 9, 35, 35, 42, 42, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 389 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114023 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114023 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114023/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114023/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114023 Building REAL300020114024 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114024' /scratch/stefan/7770410/working/building/REAL300020114024 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114024 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114024/0 /scratch/stefan/7770410/working/building/REAL300020114024 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1666) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1666 `/scratch/stefan/7770410/working/3D/1666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COC1CCCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114024.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114024 none O=C(COC1CCCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 15, 27, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 8, 8, 8, 24, 36, 36, 36, 36, 36, 8, 8, 1, 15, 15, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 5, 1, 1, 1, 1, 8, 24, 24, 36, 36, 1, 1] 201 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 44, 50, 51, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 271 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114024 none O=C(COC1CCCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 53, 85, 113, 113, 113, 113, 113, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 53, 53, 113, 113, 113, 113, 113, 113, 113, 113, 113, 113, 113, 19, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [45, 14, 13, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 391 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114024 none O=C(COC1CCCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 9, 3, 1, 1, 1, 1, 1, 1, 1, 19, 19, 40, 40, 40, 113, 113, 113, 165, 201, 201, 201, 201, 201, 113, 113, 40, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 40, 40, 40, 40, 113, 165, 165, 201, 201, 40, 40] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 39, 37, 35, 36, 38, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 732 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114024 none O=C(COC1CCCCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 128, 161, 201, 201, 201, 201, 201, 36, 36, 36, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 36, 128, 128, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 55, 36, 36, 36, 36, 8, 4, 4, 2, 2, 36, 36] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 715 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114024 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114024/1 /scratch/stefan/7770410/working/building/REAL300020114024 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1667) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1667 `/scratch/stefan/7770410/working/3D/1667' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COC1CCCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114024.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114024 none O=C(COC1CCCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 15, 27, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 8, 8, 8, 24, 36, 36, 36, 36, 36, 8, 8, 1, 15, 15, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 1, 1, 1, 1, 8, 24, 24, 36, 36, 1, 1] 201 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 44, 50, 51, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 267 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114024 none O=C(COC1CCCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 53, 86, 113, 113, 113, 113, 113, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 53, 53, 113, 113, 113, 113, 113, 113, 113, 113, 113, 113, 113, 18, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [45, 14, 13, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 390 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114024 none O=C(COC1CCCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 9, 3, 1, 1, 1, 1, 1, 1, 1, 19, 19, 39, 39, 39, 113, 113, 113, 166, 201, 201, 201, 201, 201, 113, 113, 39, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 39, 39, 39, 39, 113, 166, 166, 201, 201, 39, 39] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 39, 37, 35, 36, 38, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 731 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114024 none O=C(COC1CCCCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 128, 161, 201, 201, 201, 201, 201, 36, 36, 36, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 36, 128, 128, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 55, 36, 36, 36, 36, 8, 4, 4, 2, 2, 36, 36] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 715 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114024 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114024 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114024/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114024/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114024 Building REAL300020114025 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114025' /scratch/stefan/7770410/working/building/REAL300020114025 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114025 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114025/0 /scratch/stefan/7770410/working/building/REAL300020114025 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1668) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1668 `/scratch/stefan/7770410/working/3D/1668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCOCC(F)(F)F)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114025.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114025 none O=C(CCOCC(F)(F)F)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 15, 15, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 85, 89, 99, 108, 108, 108, 108, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 8, 85, 85, 89, 89, 108, 108, 21, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [38, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 421 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114025 none O=C(CCOCC(F)(F)F)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 15, 15, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 189, 194, 200, 201, 201, 201, 201, 44, 44, 44, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 44, 189, 189, 194, 194, 201, 201, 77, 44, 44, 44, 44, 10, 6, 6, 4, 4, 44, 44] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 726 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114025 none O=C(CCOCC(F)(F)F)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 15, 15, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 25, 27, 37, 50, 50, 50, 50, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 38, 38, 38, 38, 8, 8, 1, 25, 25, 27, 27, 50, 50, 5, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 44, 10, 11, 12, 13, 14, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 336 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114025 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114025/1 /scratch/stefan/7770410/working/building/REAL300020114025 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1669) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1669 `/scratch/stefan/7770410/working/3D/1669' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCOCC(F)(F)F)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114025.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114025/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114025 none O=C(CCOCC(F)(F)F)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 15, 15, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 85, 89, 99, 109, 109, 109, 109, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 8, 85, 85, 89, 89, 109, 109, 21, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [38, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 427 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114025 none O=C(CCOCC(F)(F)F)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 15, 15, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 189, 194, 200, 201, 201, 201, 201, 44, 44, 44, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 44, 189, 189, 194, 194, 201, 201, 77, 44, 44, 44, 44, 11, 6, 6, 4, 4, 44, 44] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 726 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114025 none O=C(CCOCC(F)(F)F)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 15, 15, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 25, 27, 37, 50, 50, 50, 50, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 38, 38, 38, 38, 8, 8, 1, 25, 25, 27, 27, 50, 50, 5, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 44, 10, 11, 12, 13, 14, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 336 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114025 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114025 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114025/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114025/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114025 Building REAL300020114026 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114026' /scratch/stefan/7770410/working/building/REAL300020114026 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114026 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114026/0 /scratch/stefan/7770410/working/building/REAL300020114026 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1670) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1670 `/scratch/stefan/7770410/working/3D/1670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCOCC1CCCO1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114026.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114026 none O=C(CCOCC1CCCO1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 5, 5, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 22, 23, 30, 43, 51, 51, 51, 51, 1, 1, 1, 1, 1, 7, 7, 7, 21, 33, 33, 33, 33, 33, 7, 7, 1, 22, 22, 23, 23, 43, 43, 51, 51, 51, 51, 51, 51, 51, 5, 1, 1, 1, 1, 7, 21, 21, 33, 33, 1, 1] 201 rigid atoms, others: [45, 43, 44, 42, 11, 12, 13, 14, 15, 51, 52, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50]) total number of confs: 323 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114026 none O=C(CCOCC1CCCO1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 5, 5, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 66, 67, 80, 101, 113, 113, 113, 113, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 66, 66, 67, 67, 101, 101, 113, 113, 113, 113, 113, 113, 113, 19, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [46, 15, 16, 17, 18, 14, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 451 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114026 none O=C(CCOCC1CCCO1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 5, 5, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 25, 16, 10, 6, 1, 1, 1, 1, 1, 1, 35, 35, 51, 51, 51, 113, 113, 113, 164, 201, 201, 201, 201, 201, 113, 113, 51, 25, 25, 16, 16, 6, 6, 1, 1, 1, 1, 1, 1, 1, 35, 51, 51, 51, 51, 113, 164, 164, 201, 201, 51, 51] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 39, 40, 38, 37] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 781 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114026 none O=C(CCOCC1CCCO1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 5, 5, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 142, 142, 153, 182, 201, 201, 201, 201, 33, 33, 33, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 33, 142, 142, 142, 142, 182, 182, 201, 201, 201, 201, 201, 201, 201, 58, 33, 33, 33, 33, 8, 4, 4, 2, 2, 33, 33] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 778 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114026 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114026/1 /scratch/stefan/7770410/working/building/REAL300020114026 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1671) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1671 `/scratch/stefan/7770410/working/3D/1671' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCOCC1CCCO1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114026.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114026/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114026 none O=C(CCOCC1CCCO1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 5, 5, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 22, 23, 30, 43, 51, 51, 51, 51, 1, 1, 1, 1, 1, 7, 7, 7, 21, 33, 33, 33, 33, 33, 7, 7, 1, 22, 22, 23, 23, 43, 43, 51, 51, 51, 51, 51, 51, 51, 5, 1, 1, 1, 1, 7, 21, 21, 33, 33, 1, 1] 201 rigid atoms, others: [45, 43, 44, 42, 11, 12, 13, 14, 15, 51, 52, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50]) total number of confs: 323 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114026 none O=C(CCOCC1CCCO1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 5, 5, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 66, 67, 80, 101, 113, 113, 113, 113, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 66, 66, 67, 67, 101, 101, 113, 113, 113, 113, 113, 113, 113, 19, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [46, 15, 16, 17, 18, 14, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 451 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114026 none O=C(CCOCC1CCCO1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 5, 5, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 25, 16, 10, 6, 1, 1, 1, 1, 1, 1, 35, 35, 51, 51, 51, 113, 113, 113, 164, 201, 201, 201, 201, 201, 113, 113, 51, 25, 25, 16, 16, 6, 6, 1, 1, 1, 1, 1, 1, 1, 35, 51, 51, 51, 51, 113, 164, 164, 201, 201, 51, 51] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 39, 40, 38, 37] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 778 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114026 none O=C(CCOCC1CCCO1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 5, 5, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 141, 141, 151, 182, 201, 201, 201, 201, 33, 33, 33, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 33, 141, 141, 141, 141, 182, 182, 201, 201, 201, 201, 201, 201, 201, 58, 33, 33, 33, 33, 8, 4, 4, 2, 2, 33, 33] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 783 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114026 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114026 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114026/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114026/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114026 Building REAL300020114027 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114027' /scratch/stefan/7770410/working/building/REAL300020114027 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114027 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114027/0 /scratch/stefan/7770410/working/building/REAL300020114027 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1672) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1672 `/scratch/stefan/7770410/working/3D/1672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CC=NC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114027.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114027 none O=C(CCC1=CC=NC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 23, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 8, 8, 8, 24, 37, 39, 39, 39, 39, 8, 8, 1, 23, 23, 31, 31, 31, 31, 31, 31, 5, 1, 1, 1, 1, 8, 24, 24, 37, 37, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 284 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114027 none O=C(CCC1=CC=NC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 94, 111, 111, 111, 111, 111, 111, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 8, 94, 94, 111, 111, 111, 111, 111, 111, 21, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 454 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114027 none O=C(CCC1=CC=NC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 4, 2, 1, 1, 1, 1, 1, 1, 1, 14, 14, 31, 31, 31, 111, 111, 111, 165, 201, 201, 201, 201, 201, 111, 111, 31, 4, 4, 2, 2, 1, 1, 1, 1, 14, 31, 31, 31, 31, 111, 165, 165, 201, 201, 31, 31] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 709 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114027 none O=C(CCC1=CC=NC=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 183, 201, 201, 201, 201, 201, 201, 39, 39, 39, 9, 9, 9, 6, 4, 1, 1, 1, 1, 1, 1, 9, 9, 39, 183, 183, 201, 201, 201, 201, 201, 201, 72, 39, 39, 39, 39, 9, 6, 6, 4, 4, 39, 39] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 780 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114027 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114027/1 /scratch/stefan/7770410/working/building/REAL300020114027 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1673) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1673 `/scratch/stefan/7770410/working/3D/1673' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CC=NC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114027.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114027 none O=C(CCC1=CC=NC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 23, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 8, 8, 8, 24, 37, 39, 39, 39, 39, 8, 8, 1, 23, 23, 31, 31, 31, 31, 31, 31, 5, 1, 1, 1, 1, 8, 24, 24, 37, 37, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 284 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114027 none O=C(CCC1=CC=NC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 95, 111, 111, 111, 111, 111, 111, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 8, 95, 95, 111, 111, 111, 111, 111, 111, 21, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 451 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114027 none O=C(CCC1=CC=NC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 4, 2, 1, 1, 1, 1, 1, 1, 1, 14, 14, 31, 31, 31, 111, 111, 111, 165, 201, 201, 201, 201, 201, 111, 111, 31, 4, 4, 2, 2, 1, 1, 1, 1, 14, 31, 31, 31, 31, 111, 165, 165, 201, 201, 31, 31] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 711 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114027 none O=C(CCC1=CC=NC=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 184, 201, 201, 201, 201, 201, 201, 39, 39, 39, 9, 9, 9, 6, 4, 1, 1, 1, 1, 1, 1, 9, 9, 39, 184, 184, 201, 201, 201, 201, 201, 201, 72, 39, 39, 39, 39, 9, 6, 6, 4, 4, 39, 39] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 783 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114027 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114027 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114027/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114027/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114027 Building REAL300020114028 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114028' /scratch/stefan/7770410/working/building/REAL300020114028 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114028 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114028/0 /scratch/stefan/7770410/working/building/REAL300020114028 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1674) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1674 `/scratch/stefan/7770410/working/3D/1674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)N1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1) `REAL300020114028.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114028 none CC(C)(C)N1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [25, 16, 25, 25, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 22, 31, 37, 37, 37, 37, 6, 6, 1, 16, 16, 25, 25, 25, 25, 25, 25, 25, 25, 25, 16, 6, 1, 1, 1, 1, 6, 22, 22, 31, 31, 1, 1, 16] 73 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 48, 49, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50]) total number of confs: 205 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114028 none CC(C)(C)N1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [46, 33, 46, 46, 33, 33, 18, 18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 8, 11, 16, 16, 16, 16, 1, 1, 6, 33, 33, 46, 46, 46, 46, 46, 46, 46, 46, 46, 33, 18, 6, 6, 6, 6, 1, 8, 8, 11, 11, 6, 6, 33] 73 rigid atoms, others: [43, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 189 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114028 none CC(C)(C)N1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 33, 33, 33, 61, 70, 73, 73, 73, 73, 33, 33, 16, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 5, 16, 16, 16, 16, 33, 61, 61, 70, 70, 16, 16, 1] 73 rigid atoms, others: [1, 4, 5, 6, 7, 50, 26, 27, 37] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114028 none CC(C)(C)N1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 73, 73, 73, 54, 54, 54, 38, 38, 38, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 38, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 54, 38, 38, 38, 38, 18, 6, 6, 4, 4, 38, 38, 73] 73 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 189 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114028 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114028/1 /scratch/stefan/7770410/working/building/REAL300020114028 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1675) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1675 `/scratch/stefan/7770410/working/3D/1675' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)N1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1) `REAL300020114028.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114028 none CC(C)(C)N1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [25, 16, 25, 25, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 22, 31, 37, 37, 37, 37, 6, 6, 1, 16, 16, 25, 25, 25, 25, 25, 25, 25, 25, 25, 16, 6, 1, 1, 1, 1, 6, 22, 22, 31, 31, 1, 1, 16] 73 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 48, 49, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50]) total number of confs: 205 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114028 none CC(C)(C)N1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [47, 33, 47, 47, 33, 33, 18, 18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 8, 11, 16, 16, 16, 16, 1, 1, 6, 33, 33, 47, 47, 47, 47, 47, 47, 47, 47, 47, 33, 18, 6, 6, 6, 6, 1, 8, 8, 11, 11, 6, 6, 33] 73 rigid atoms, others: [43, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 192 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114028 none CC(C)(C)N1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 33, 33, 33, 61, 70, 73, 73, 73, 73, 33, 33, 16, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 5, 16, 16, 16, 16, 33, 61, 61, 70, 70, 16, 16, 1] 73 rigid atoms, others: [1, 4, 5, 6, 7, 50, 26, 27, 37] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114028 none CC(C)(C)N1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 73, 73, 73, 54, 54, 54, 38, 38, 38, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 38, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 54, 38, 38, 38, 38, 18, 6, 6, 4, 4, 38, 38, 73] 73 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 189 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114028 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114028 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114028/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114028/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114028 Building REAL300020114029 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114029' /scratch/stefan/7770410/working/building/REAL300020114029 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114029 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114029/0 /scratch/stefan/7770410/working/building/REAL300020114029 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1676) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1676 `/scratch/stefan/7770410/working/3D/1676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC(=O)NC1) `REAL300020114029.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114029 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC(=O)NC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 11, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 33, 103, 103, 103, 103, 103, 103, 33, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 103, 103, 103, 103, 103, 103, 103, 103] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 300 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114029 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC(=O)NC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 11, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 58, 58, 58, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 58, 108, 201, 201, 201, 201, 201, 201, 108, 58, 58, 58, 58, 12, 6, 6, 4, 4, 58, 58, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 604 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114029 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC(=O)NC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 11, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 34, 49, 57, 57, 57, 57, 11, 11, 1, 6, 27, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 11, 34, 34, 49, 49, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114029 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCC(=O)NC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 11, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 27, 27, 27, 103, 103, 103, 166, 201, 201, 201, 201, 201, 103, 103, 27, 1, 1, 1, 1, 1, 1, 1, 10, 27, 27, 27, 27, 103, 166, 166, 201, 201, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 38, 39, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 714 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114029 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114029/1 /scratch/stefan/7770410/working/building/REAL300020114029 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1677) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1677 `/scratch/stefan/7770410/working/3D/1677' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC(=O)NC1) `REAL300020114029.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114029 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC(=O)NC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 11, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 33, 101, 101, 101, 101, 101, 101, 33, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 101, 101, 101, 101, 101, 101, 101, 101] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 294 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114029 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC(=O)NC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 11, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 58, 58, 58, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 58, 106, 201, 201, 201, 201, 201, 201, 106, 58, 58, 58, 58, 12, 6, 6, 4, 4, 58, 58, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 602 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114029 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC(=O)NC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 11, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 34, 49, 57, 57, 57, 57, 11, 11, 1, 6, 27, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 11, 34, 34, 49, 49, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114029 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCC(=O)NC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 11, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 27, 27, 27, 101, 101, 101, 165, 201, 201, 201, 201, 201, 101, 101, 27, 1, 1, 1, 1, 1, 1, 1, 10, 27, 27, 27, 27, 101, 165, 165, 201, 201, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 38, 39, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 726 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114029 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114029 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114029/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114029/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114029 Building REAL300020114030 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114030' /scratch/stefan/7770410/working/building/REAL300020114030 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114030 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114030/0 /scratch/stefan/7770410/working/building/REAL300020114030 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1678) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1678 `/scratch/stefan/7770410/working/3D/1678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[N@@H+]1CCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114030.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114030 none CC(C)C[N@@H+]1CCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 12, 12, 12, 12, 12, 12, 10, 10, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 10, 12, 12, 12, 12, 1, 1] 53 rigid atoms, others: [16, 12, 13, 46, 15, 48, 49, 14, 55, 56, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53, 54]) total number of confs: 61 number of broken/clashed sets: 52 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114030 none CC(C)C[N@@H+]1CCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 52, 52, 52, 52, 52, 52, 39, 39, 39, 10, 10, 10, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 10, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 39, 10, 10, 10, 10, 1, 4, 4, 4, 4, 10, 10] 53 rigid atoms, others: [50, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56]) total number of confs: 157 number of broken/clashed sets: 52 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114030 none CC(C)C[N@@H+]1CCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 52, 52, 52, 53, 53, 53, 53, 53, 53, 52, 52, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 14, 14, 14, 14, 52, 53, 53, 53, 53, 14, 14] 53 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 42, 39, 44, 40, 43, 41, 38, 10] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 94 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114030 none CC(C)C[N@@H+]1CCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 53, 53, 53, 53, 41, 41, 41, 14, 14, 14, 6, 6, 6, 5, 2, 1, 1, 1, 1, 1, 1, 6, 6, 14, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 41, 14, 14, 14, 14, 6, 5, 5, 2, 2, 14, 14] 53 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 168 number of broken/clashed sets: 52 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114030 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114030/1 /scratch/stefan/7770410/working/building/REAL300020114030 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1679) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1679 `/scratch/stefan/7770410/working/3D/1679' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[N@H+]1CCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114030.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114030 none CC(C)C[N@H+]1CCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1] 15 rigid atoms, others: [16, 12, 13, 46, 15, 48, 49, 14, 55, 56, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53, 54]) total number of confs: 23 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114030 none CC(C)C[N@H+]1CCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 14, 14, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 8, 8, 8, 8, 1, 3, 3, 3, 3, 8, 8] 15 rigid atoms, others: [50, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56]) total number of confs: 50 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114030 none CC(C)C[N@H+]1CCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 6, 15, 15, 15, 15, 15, 6, 6] 15 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 42, 39, 44, 40, 43, 41, 38, 10] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114030 none CC(C)C[N@H+]1CCCC1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 14, 14, 8, 8, 8, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 8, 8, 8, 8, 3, 3, 3, 1, 1, 8, 8] 15 rigid atoms, others: [22, 19, 20, 21, 54, 23, 24, 25, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 55, 56]) total number of confs: 48 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114030 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114030 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114030/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114030/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114030 Building REAL300020114031 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114031' /scratch/stefan/7770410/working/building/REAL300020114031 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114031 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114031/0 /scratch/stefan/7770410/working/building/REAL300020114031 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1680) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1680 `/scratch/stefan/7770410/working/3D/1680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC=N1) `REAL300020114031.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114031 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 30, 44, 47, 47, 47, 47, 11, 11, 1, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 11, 30, 30, 44, 44, 1, 1, 13, 13] 201 rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44]) total number of confs: 205 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114031 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 76, 28, 28, 28, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 76, 76, 76, 76, 76, 76, 76, 28, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 76, 76] 201 rigid atoms, others: [36, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 175 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114031 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 76, 76, 76, 146, 201, 201, 201, 201, 201, 76, 76, 13, 1, 1, 1, 2, 2, 2, 1, 5, 13, 13, 13, 13, 76, 146, 146, 201, 201, 13, 13, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 44, 24, 25, 26, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 808 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114031 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 79, 79, 79, 47, 47, 47, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 47, 201, 201, 201, 201, 201, 201, 201, 79, 47, 47, 47, 47, 10, 6, 6, 4, 4, 47, 47, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 405 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114031 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114031/1 /scratch/stefan/7770410/working/building/REAL300020114031 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1681) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1681 `/scratch/stefan/7770410/working/3D/1681' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC=N1) `REAL300020114031.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114031/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114031 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 30, 44, 47, 47, 47, 47, 11, 11, 1, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 11, 30, 30, 44, 44, 1, 1, 13, 13] 201 rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44]) total number of confs: 205 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114031 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 76, 28, 28, 28, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 76, 76, 76, 76, 76, 76, 76, 28, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 76, 76] 201 rigid atoms, others: [36, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 175 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114031 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 76, 76, 76, 146, 201, 201, 201, 201, 201, 76, 76, 13, 1, 1, 1, 2, 2, 2, 1, 5, 13, 13, 13, 13, 76, 146, 146, 201, 201, 13, 13, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 44, 24, 25, 26, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 808 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114031 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 79, 79, 79, 47, 47, 47, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 47, 201, 201, 201, 201, 201, 201, 201, 79, 47, 47, 47, 47, 10, 6, 6, 4, 4, 47, 47, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 405 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114031 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114031 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114031/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114031/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114031 Building REAL300020114032 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114032' /scratch/stefan/7770410/working/building/REAL300020114032 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114032 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114032/0 /scratch/stefan/7770410/working/building/REAL300020114032 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1682) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1682 `/scratch/stefan/7770410/working/3D/1682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1) `REAL300020114032.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114032 none CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 15, 28, 15, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 30, 44, 50, 50, 50, 50, 11, 11, 1, 15, 15, 28, 28, 28, 28, 28, 28, 15, 15, 6, 1, 1, 1, 1, 11, 30, 30, 44, 44, 1, 1, 15] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48]) total number of confs: 259 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114032 none CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 72, 115, 72, 72, 72, 29, 29, 29, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 11, 11, 11, 11, 1, 1, 11, 72, 72, 115, 115, 115, 115, 115, 115, 72, 72, 29, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 72] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 332 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114032 none CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 72, 72, 72, 153, 197, 201, 201, 201, 201, 72, 72, 15, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 5, 15, 15, 15, 15, 72, 153, 153, 197, 197, 15, 15, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 48, 35, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 776 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114032 none CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 96, 96, 96, 52, 52, 52, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 52, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 96, 52, 52, 52, 52, 12, 6, 6, 4, 4, 52, 52, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 422 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114032 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114032/1 /scratch/stefan/7770410/working/building/REAL300020114032 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1683) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1683 `/scratch/stefan/7770410/working/3D/1683' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1) `REAL300020114032.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114032 none CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 15, 28, 15, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 30, 44, 50, 50, 50, 50, 11, 11, 1, 15, 15, 28, 28, 28, 28, 28, 28, 15, 15, 6, 1, 1, 1, 1, 11, 30, 30, 44, 44, 1, 1, 15] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48]) total number of confs: 259 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114032 none CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 71, 114, 71, 71, 71, 29, 29, 29, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 71, 71, 114, 114, 114, 114, 114, 114, 71, 71, 29, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 71] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 328 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114032 none CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 71, 71, 71, 153, 197, 201, 201, 201, 201, 71, 71, 15, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 5, 15, 15, 15, 15, 71, 153, 153, 197, 197, 15, 15, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 48, 35, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 781 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114032 none CN(C)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 96, 96, 96, 51, 51, 51, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 51, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 96, 51, 51, 51, 51, 11, 6, 6, 4, 4, 51, 51, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 424 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114032 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114032 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114032/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114032/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114032 Building REAL300020114033 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114033' /scratch/stefan/7770410/working/building/REAL300020114033 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114033 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114033/0 /scratch/stefan/7770410/working/building/REAL300020114033 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1684) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1684 `/scratch/stefan/7770410/working/3D/1684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=NNC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114033.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114033 none CCCC1=NNC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [64, 49, 21, 21, 21, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 24, 32, 43, 43, 43, 43, 5, 5, 1, 64, 64, 64, 64, 64, 49, 49, 21, 21, 6, 1, 1, 1, 1, 5, 24, 24, 32, 32, 1, 1] 185 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 390 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114033 none CCCC1=NNC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [108, 97, 49, 49, 49, 49, 49, 19, 19, 19, 5, 5, 5, 1, 1, 1, 1, 1, 8, 10, 14, 14, 14, 14, 1, 1, 5, 108, 108, 108, 108, 108, 97, 97, 49, 49, 19, 5, 5, 5, 5, 1, 8, 8, 10, 10, 5, 5] 185 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 437 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114033 none CCCC1=NNC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 21, 21, 21, 49, 49, 49, 101, 124, 136, 136, 136, 136, 49, 49, 21, 10, 10, 10, 9, 9, 5, 5, 1, 1, 8, 21, 21, 21, 21, 49, 101, 101, 124, 124, 21, 21] 185 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 34, 35] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 518 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114033 none CCCC1=NNC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [176, 176, 131, 131, 131, 131, 131, 88, 88, 88, 45, 45, 45, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 45, 176, 176, 176, 176, 176, 176, 176, 131, 131, 88, 45, 45, 45, 45, 17, 6, 6, 4, 4, 45, 45] 176 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 604 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114033 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114033/1 /scratch/stefan/7770410/working/building/REAL300020114033 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1685) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1685 `/scratch/stefan/7770410/working/3D/1685' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=NNC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114033.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114033/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114033 none CCCC1=NNC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [65, 50, 21, 21, 21, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 23, 31, 42, 42, 42, 42, 5, 5, 1, 65, 65, 65, 65, 65, 50, 50, 21, 21, 6, 1, 1, 1, 1, 5, 23, 23, 31, 31, 1, 1] 183 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 393 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114033 none CCCC1=NNC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [108, 98, 49, 49, 49, 49, 49, 19, 19, 19, 5, 5, 5, 1, 1, 1, 1, 1, 8, 10, 14, 14, 14, 14, 1, 1, 5, 108, 108, 108, 108, 108, 98, 98, 49, 49, 19, 5, 5, 5, 5, 1, 8, 8, 10, 10, 5, 5] 183 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 437 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114033 none CCCC1=NNC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 21, 21, 21, 49, 49, 49, 98, 121, 133, 133, 133, 133, 49, 49, 21, 10, 10, 10, 9, 9, 5, 5, 1, 1, 8, 21, 21, 21, 21, 49, 98, 98, 121, 121, 21, 21] 183 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 34, 35] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 506 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114033 none CCCC1=NNC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [174, 174, 129, 129, 129, 129, 129, 86, 86, 86, 44, 44, 44, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 44, 174, 174, 174, 174, 174, 174, 174, 129, 129, 86, 44, 44, 44, 44, 17, 6, 6, 4, 4, 44, 44] 174 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 598 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114033 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114033 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114033/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114033/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114033 Building REAL300020114034 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114034' /scratch/stefan/7770410/working/building/REAL300020114034 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114034 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114034/0 /scratch/stefan/7770410/working/building/REAL300020114034 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1686) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1686 `/scratch/stefan/7770410/working/3D/1686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NNC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114034.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114034 none CCC1=NNC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [33, 17, 17, 17, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 23, 32, 45, 45, 45, 45, 5, 5, 1, 33, 33, 33, 33, 33, 17, 17, 6, 1, 1, 1, 1, 5, 23, 23, 32, 32, 1, 1] 118 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 260 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114034 none CCC1=NNC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [61, 31, 31, 31, 31, 31, 16, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 8, 12, 17, 17, 17, 17, 1, 1, 5, 61, 61, 61, 61, 61, 31, 31, 16, 5, 5, 5, 5, 1, 8, 8, 12, 12, 5, 5] 118 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 282 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114034 none CCC1=NNC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 17, 31, 31, 31, 68, 80, 84, 84, 84, 84, 31, 31, 17, 4, 4, 4, 4, 4, 1, 1, 7, 17, 17, 17, 17, 31, 68, 68, 80, 80, 17, 17] 118 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 326 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114034 none CCC1=NNC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [117, 79, 79, 79, 79, 79, 71, 71, 71, 46, 46, 46, 20, 20, 20, 6, 4, 1, 1, 1, 1, 1, 1, 20, 20, 46, 117, 117, 117, 117, 117, 79, 79, 71, 46, 46, 46, 46, 20, 6, 6, 4, 4, 46, 46] 117 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 443 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114034 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114034/1 /scratch/stefan/7770410/working/building/REAL300020114034 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1687) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1687 `/scratch/stefan/7770410/working/3D/1687' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NNC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114034.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114034/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114034 none CCC1=NNC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [32, 17, 17, 17, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 23, 32, 45, 45, 45, 45, 5, 5, 1, 32, 32, 32, 32, 32, 17, 17, 6, 1, 1, 1, 1, 5, 23, 23, 32, 32, 1, 1] 117 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 257 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114034 none CCC1=NNC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [60, 31, 31, 31, 31, 31, 16, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 8, 12, 17, 17, 17, 17, 1, 1, 5, 60, 60, 60, 60, 60, 31, 31, 16, 5, 5, 5, 5, 1, 8, 8, 12, 12, 5, 5] 117 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 279 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114034 none CCC1=NNC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 17, 31, 31, 31, 68, 80, 84, 84, 84, 84, 31, 31, 17, 4, 4, 4, 4, 4, 1, 1, 7, 17, 17, 17, 17, 31, 68, 68, 80, 80, 17, 17] 117 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 323 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114034 none CCC1=NNC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [117, 84, 84, 84, 84, 84, 74, 74, 74, 47, 47, 47, 20, 20, 20, 6, 4, 1, 1, 1, 1, 1, 1, 20, 20, 47, 117, 117, 117, 117, 117, 84, 84, 74, 47, 47, 47, 47, 20, 6, 6, 4, 4, 47, 47] 117 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 429 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114034 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114034 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114034/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114034/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114034 Building REAL300020114035 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114035' /scratch/stefan/7770410/working/building/REAL300020114035 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114035 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114035/0 /scratch/stefan/7770410/working/building/REAL300020114035 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1688) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1688 `/scratch/stefan/7770410/working/3D/1688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NNC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114035.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114035 none CC(C)C1=NNC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 32, 47, 56, 56, 56, 56, 11, 11, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 32, 32, 47, 47, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 240 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114035 none CC(C)C1=NNC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 102, 102, 102, 102, 33, 33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 102, 102, 102, 102, 102, 102, 102, 102, 102, 33, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 210 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114035 none CC(C)C1=NNC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 22, 22, 22, 102, 102, 102, 154, 201, 201, 201, 201, 201, 102, 102, 22, 2, 2, 2, 2, 2, 2, 2, 1, 1, 7, 22, 22, 22, 22, 102, 154, 154, 201, 201, 22, 22] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 35] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 724 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114035 none CC(C)C1=NNC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 107, 107, 107, 56, 56, 56, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 56, 201, 201, 201, 201, 201, 201, 201, 201, 201, 107, 56, 56, 56, 56, 10, 6, 6, 4, 4, 56, 56] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 466 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114035 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114035/1 /scratch/stefan/7770410/working/building/REAL300020114035 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1689) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1689 `/scratch/stefan/7770410/working/3D/1689' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NNC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114035.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114035 none CC(C)C1=NNC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 32, 47, 56, 56, 56, 56, 11, 11, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 32, 32, 47, 47, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 240 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114035 none CC(C)C1=NNC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 102, 102, 102, 102, 33, 33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 102, 102, 102, 102, 102, 102, 102, 102, 102, 33, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 210 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114035 none CC(C)C1=NNC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 22, 22, 22, 102, 102, 102, 154, 201, 201, 201, 201, 201, 102, 102, 22, 2, 2, 2, 2, 2, 2, 2, 1, 1, 7, 22, 22, 22, 22, 102, 154, 154, 201, 201, 22, 22] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 35] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 724 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114035 none CC(C)C1=NNC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 107, 107, 107, 56, 56, 56, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 56, 201, 201, 201, 201, 201, 201, 201, 201, 201, 107, 56, 56, 56, 56, 10, 6, 6, 4, 4, 56, 56] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 466 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114035 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114035 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114035/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114035/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114035 Building REAL300020114036 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114036' /scratch/stefan/7770410/working/building/REAL300020114036 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114036 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114036/0 /scratch/stefan/7770410/working/building/REAL300020114036 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1690) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1690 `/scratch/stefan/7770410/working/3D/1690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=NNC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020114036.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114036 none CC(C)(C)C1=NNC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 13, 27, 27, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 53, 71, 93, 93, 93, 93, 12, 12, 1, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 13, 6, 1, 1, 1, 1, 12, 53, 53, 71, 71, 1, 1, 13] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50]) total number of confs: 406 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114036 none CC(C)(C)C1=NNC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 65, 113, 113, 65, 65, 65, 48, 48, 48, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 12, 65, 113, 113, 113, 113, 113, 113, 113, 113, 113, 65, 48, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 65] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 449 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114036 none CC(C)(C)C1=NNC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 65, 65, 65, 141, 185, 201, 201, 201, 201, 65, 65, 13, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 5, 13, 13, 13, 13, 65, 141, 141, 185, 185, 13, 13, 1] 201 rigid atoms, others: [1, 4, 5, 6, 7, 8, 50, 27, 37] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 737 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114036 none CC(C)(C)C1=NNC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 190, 190, 190, 93, 93, 93, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 93, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 190, 93, 93, 93, 93, 18, 6, 6, 4, 4, 93, 93, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 541 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114036 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114036/1 /scratch/stefan/7770410/working/building/REAL300020114036 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1691) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1691 `/scratch/stefan/7770410/working/3D/1691' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=NNC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020114036.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114036 none CC(C)(C)C1=NNC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 13, 27, 27, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 54, 72, 95, 95, 95, 95, 12, 12, 1, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 13, 6, 1, 1, 1, 1, 12, 54, 54, 72, 72, 1, 1, 13] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50]) total number of confs: 411 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114036 none CC(C)(C)C1=NNC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 65, 112, 112, 65, 65, 65, 48, 48, 48, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 12, 65, 112, 112, 112, 112, 112, 112, 112, 112, 112, 65, 48, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 65] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 440 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114036 none CC(C)(C)C1=NNC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 65, 65, 65, 141, 185, 201, 201, 201, 201, 65, 65, 13, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 5, 13, 13, 13, 13, 65, 141, 141, 185, 185, 13, 13, 1] 201 rigid atoms, others: [1, 4, 5, 6, 7, 8, 50, 27, 37] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 740 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114036 none CC(C)(C)C1=NNC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 190, 190, 190, 94, 94, 94, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 94, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 190, 94, 94, 94, 94, 17, 6, 6, 4, 4, 94, 94, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 540 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114036 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114036 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114036/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114036/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114036 Building REAL300020114037 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114037' /scratch/stefan/7770410/working/building/REAL300020114037 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114037 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114037/0 /scratch/stefan/7770410/working/building/REAL300020114037 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1692) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1692 `/scratch/stefan/7770410/working/3D/1692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NNC2=C1CCC2) `REAL300020114037.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114037 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NNC2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 3, 7, 10, 10, 10, 10, 10, 10, 10, 7, 3, 3, 3, 3, 1, 4, 4, 4, 4, 3, 3, 10, 10, 10, 10, 10, 10, 10] 11 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 36 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114037 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NNC2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 5, 5, 5, 5, 5, 5, 4, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 11, 11, 11, 11, 11, 11, 11, 9, 5, 5, 5, 5, 5, 4, 4, 2, 2, 5, 5, 11, 11, 11, 11, 11, 11, 11] 11 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 33 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114037 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NNC2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 3, 3, 1, 6, 10, 10, 10, 10, 10, 10, 10, 6, 1, 1, 1, 1, 3, 4, 4, 4, 4, 1, 1, 10, 10, 10, 10, 10, 10, 10] 11 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114037 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NNC2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 5, 10, 10, 10, 10, 10, 11, 11, 11, 11, 10, 10, 1, 1, 1, 1, 1, 1, 1] 11 rigid atoms, others: [1, 39, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 33 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114037 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114037/1 /scratch/stefan/7770410/working/building/REAL300020114037 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1693) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1693 `/scratch/stefan/7770410/working/3D/1693' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NNC2=C1CCC2) `REAL300020114037.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114037 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NNC2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 3, 8, 11, 11, 11, 11, 11, 11, 11, 8, 3, 3, 3, 3, 1, 4, 4, 4, 4, 3, 3, 11, 11, 11, 11, 11, 11, 11] 12 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114037 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NNC2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 5, 5, 5, 5, 5, 5, 4, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 12, 12, 12, 12, 12, 12, 12, 10, 5, 5, 5, 5, 5, 4, 4, 2, 2, 5, 5, 12, 12, 12, 12, 12, 12, 12] 12 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 35 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114037 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NNC2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 3, 3, 1, 6, 11, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 3, 4, 4, 4, 4, 1, 1, 11, 11, 11, 11, 11, 11, 11] 12 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114037 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NNC2=C1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 11, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 6, 11, 11, 11, 11, 11, 12, 12, 12, 12, 11, 11, 1, 1, 1, 1, 1, 1, 1] 12 rigid atoms, others: [1, 39, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 35 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114037 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114037 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114037/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114037/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114037 Building REAL300020114038 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114038' /scratch/stefan/7770410/working/building/REAL300020114038 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114038 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114038/0 /scratch/stefan/7770410/working/building/REAL300020114038 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1694) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1694 `/scratch/stefan/7770410/working/3D/1694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NNC2=C1CCCC2) `REAL300020114038.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114038 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NNC2=C1CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 20, 20, 20, 20, 1, 1, 13, 53, 84, 84, 84, 84, 84, 84, 84, 84, 53, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 84, 84, 84, 84, 84, 84, 84, 84, 84] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 252 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114038 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NNC2=C1CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 114, 114, 114, 22, 22, 22, 6, 4, 1, 1, 1, 1, 1, 1, 22, 22, 114, 200, 201, 201, 201, 201, 201, 201, 201, 201, 200, 114, 114, 114, 114, 22, 6, 6, 4, 4, 114, 114, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 546 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114038 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NNC2=C1CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 67, 91, 113, 113, 113, 113, 13, 13, 1, 6, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 67, 67, 91, 91, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 424 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114038 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NNC2=C1CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 16, 16, 16, 84, 84, 84, 161, 201, 201, 201, 201, 201, 84, 84, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 16, 16, 16, 16, 84, 161, 161, 201, 201, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 732 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114038 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114038/1 /scratch/stefan/7770410/working/building/REAL300020114038 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1695) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1695 `/scratch/stefan/7770410/working/3D/1695' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NNC2=C1CCCC2) `REAL300020114038.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114038 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NNC2=C1CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 20, 20, 20, 20, 1, 1, 13, 53, 84, 84, 84, 84, 84, 84, 84, 84, 53, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 84, 84, 84, 84, 84, 84, 84, 84, 84] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 252 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114038 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NNC2=C1CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 113, 113, 113, 24, 24, 24, 6, 4, 1, 1, 1, 1, 1, 1, 24, 24, 113, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 113, 113, 113, 113, 24, 6, 6, 4, 4, 113, 113, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 550 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114038 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NNC2=C1CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 67, 91, 113, 113, 113, 113, 13, 13, 1, 6, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 67, 67, 91, 91, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 424 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114038 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NNC2=C1CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 16, 16, 16, 84, 84, 84, 161, 201, 201, 201, 201, 201, 84, 84, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 16, 16, 16, 16, 84, 161, 161, 201, 201, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 732 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114038 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114038 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114038/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114038/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114038 Building REAL300020114039 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114039' /scratch/stefan/7770410/working/building/REAL300020114039 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114039 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114039/0 /scratch/stefan/7770410/working/building/REAL300020114039 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1696) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1696 `/scratch/stefan/7770410/working/3D/1696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NNN=C1) `REAL300020114039.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114039 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NNN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 3, 6, 11, 11, 11, 11, 6, 3, 3, 3, 3, 1, 5, 5, 5, 5, 3, 3, 11, 11] 13 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 29] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 40 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114039 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NNN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 5, 5, 5, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 13, 13, 13, 13, 8, 5, 5, 5, 5, 5, 3, 3, 1, 1, 5, 5, 13, 13] 13 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 33 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114039 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NNN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 3, 3, 1, 6, 11, 11, 11, 11, 6, 1, 1, 1, 1, 3, 5, 5, 5, 5, 1, 1, 11, 11] 13 rigid atoms, others: [2, 3, 4, 5, 6, 34, 18, 35, 25, 26, 27, 28] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114039 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NNN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 11, 11, 11, 11, 11, 11, 13, 13, 13, 13, 13, 13, 11, 11, 11, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 13, 13, 13, 13, 11, 11, 1, 1] 13 rigid atoms, others: [1, 36, 37, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 39 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114039 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114039/1 /scratch/stefan/7770410/working/building/REAL300020114039 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1697) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1697 `/scratch/stefan/7770410/working/3D/1697' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NNN=C1) `REAL300020114039.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114039 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NNN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 3, 6, 11, 11, 11, 11, 6, 3, 3, 3, 3, 1, 5, 5, 5, 5, 3, 3, 11, 11] 13 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 29] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 40 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114039 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NNN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 5, 5, 5, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 13, 13, 13, 13, 8, 5, 5, 5, 5, 5, 3, 3, 1, 1, 5, 5, 13, 13] 13 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 33 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114039 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NNN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 3, 3, 1, 6, 11, 11, 11, 11, 6, 1, 1, 1, 1, 3, 5, 5, 5, 5, 1, 1, 11, 11] 13 rigid atoms, others: [2, 3, 4, 5, 6, 34, 18, 35, 25, 26, 27, 28] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114039 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NNN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 11, 11, 11, 11, 11, 11, 13, 13, 13, 13, 13, 13, 11, 11, 11, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 13, 13, 13, 13, 11, 11, 1, 1] 13 rigid atoms, others: [1, 36, 37, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 39 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114039 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114039 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114039/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114039/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114039 Building REAL300020114040 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114040' /scratch/stefan/7770410/working/building/REAL300020114040 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114040 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114040/0 /scratch/stefan/7770410/working/building/REAL300020114040 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1698) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1698 `/scratch/stefan/7770410/working/3D/1698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1CCCCC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114040.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114040 none O=C(CN1CCCCC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 9, 9, 9, 34, 49, 53, 53, 53, 53, 9, 9, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 6, 1, 1, 1, 1, 9, 34, 34, 49, 49, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 312 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114040 none O=C(CN1CCCCC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 111, 111, 111, 111, 111, 111, 111, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 111, 111, 111, 111, 111, 111, 111, 111, 111, 111, 31, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 419 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114040 none O=C(CN1CCCCC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 32, 32, 32, 111, 111, 111, 179, 201, 201, 201, 201, 201, 111, 111, 32, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 12, 32, 32, 32, 32, 111, 179, 179, 201, 201, 32, 32] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 36, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 677 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114040 none O=C(CN1CCCCC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 201, 201, 201, 201, 201, 201, 201, 53, 53, 53, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 53, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 108, 53, 53, 53, 53, 12, 6, 6, 4, 4, 53, 53] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 732 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114040 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114040/1 /scratch/stefan/7770410/working/building/REAL300020114040 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1699) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1699 `/scratch/stefan/7770410/working/3D/1699' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1CCCCC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114040.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114040/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114040 none O=C(CN1CCCCC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 9, 9, 9, 34, 49, 53, 53, 53, 53, 9, 9, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 6, 1, 1, 1, 1, 9, 34, 34, 49, 49, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 312 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114040 none O=C(CN1CCCCC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 111, 111, 111, 111, 111, 111, 111, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 111, 111, 111, 111, 111, 111, 111, 111, 111, 111, 31, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 419 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114040 none O=C(CN1CCCCC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 32, 32, 32, 111, 111, 111, 179, 201, 201, 201, 201, 201, 111, 111, 32, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 12, 32, 32, 32, 32, 111, 179, 179, 201, 201, 32, 32] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 36, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 677 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114040 none O=C(CN1CCCCC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 201, 201, 201, 201, 201, 201, 201, 53, 53, 53, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 53, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 108, 53, 53, 53, 53, 11, 6, 6, 4, 4, 53, 53] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 733 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114040 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114040 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114040/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114040/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114040 Building REAL300020114041 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114041' /scratch/stefan/7770410/working/building/REAL300020114041 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114041 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114041/0 /scratch/stefan/7770410/working/building/REAL300020114041 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1700) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1700 `/scratch/stefan/7770410/working/3D/1700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(=O)NC=N1) `REAL300020114041.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114041 none CC1=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(=O)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 25, 23, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 24, 36, 36, 36, 36, 36, 8, 8, 1, 30, 30, 30, 30, 30, 30, 30, 30, 25, 25, 23, 23, 5, 1, 1, 1, 1, 8, 24, 24, 36, 36, 1, 1, 30, 30] 201 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 46, 47, 40, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49]) total number of confs: 242 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114041 none CC1=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(=O)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 90, 88, 18, 18, 18, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 101, 101, 101, 101, 101, 101, 101, 101, 90, 90, 88, 88, 18, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 101, 101] 201 rigid atoms, others: [41, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 365 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114041 none CC1=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(=O)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 15, 15, 15, 30, 30, 30, 101, 101, 101, 157, 201, 201, 201, 201, 201, 101, 101, 30, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 5, 5, 15, 30, 30, 30, 30, 101, 157, 157, 201, 201, 30, 30, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 48, 49, 24, 25, 26, 27, 28] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 754 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114041 none CC1=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(=O)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 192, 192, 62, 62, 62, 36, 36, 36, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 36, 201, 201, 201, 201, 201, 201, 201, 201, 192, 192, 192, 192, 62, 36, 36, 36, 36, 8, 4, 4, 2, 2, 36, 36, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 730 number of broken/clashed sets: 200 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114041 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114041/1 /scratch/stefan/7770410/working/building/REAL300020114041 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1701) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1701 `/scratch/stefan/7770410/working/3D/1701' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(=O)NC=N1) `REAL300020114041.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114041 none CC1=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(=O)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 25, 23, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 24, 36, 36, 36, 36, 36, 8, 8, 1, 30, 30, 30, 30, 30, 30, 30, 30, 25, 25, 23, 23, 5, 1, 1, 1, 1, 8, 24, 24, 36, 36, 1, 1, 30, 30] 201 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 46, 47, 40, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49]) total number of confs: 242 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114041 none CC1=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(=O)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 90, 88, 18, 18, 18, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 101, 101, 101, 101, 101, 101, 101, 101, 90, 90, 88, 88, 18, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 101, 101] 201 rigid atoms, others: [41, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 365 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114041 none CC1=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(=O)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 15, 15, 15, 30, 30, 30, 101, 101, 101, 157, 201, 201, 201, 201, 201, 101, 101, 30, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 5, 5, 15, 30, 30, 30, 30, 101, 157, 157, 201, 201, 30, 30, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 48, 49, 24, 25, 26, 27, 28] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 754 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114041 none CC1=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(=O)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 191, 191, 63, 63, 63, 37, 37, 37, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 37, 201, 201, 201, 201, 201, 201, 201, 201, 191, 191, 191, 191, 63, 37, 37, 37, 37, 8, 4, 4, 2, 2, 37, 37, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 722 number of broken/clashed sets: 200 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114041 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114041 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114041/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114041/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114041 Building REAL300020114042 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114042' /scratch/stefan/7770410/working/building/REAL300020114042 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114042 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114042/0 /scratch/stefan/7770410/working/building/REAL300020114042 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1702) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1702 `/scratch/stefan/7770410/working/3D/1702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CC1=O) `REAL300020114042.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114042 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 29, 44, 47, 47, 47, 47, 9, 9, 1, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 9, 29, 29, 44, 44, 1, 1, 17, 17] 201 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44]) total number of confs: 218 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114042 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 27, 27, 27, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 73, 73, 73, 73, 73, 73, 73, 73, 27, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 73, 73] 201 rigid atoms, others: [36, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 169 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114042 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 73, 73, 73, 141, 201, 201, 201, 201, 201, 73, 73, 17, 1, 1, 1, 1, 2, 2, 2, 1, 5, 17, 17, 17, 17, 73, 141, 141, 201, 201, 17, 17, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 43, 44, 23, 24, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 837 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114042 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 79, 79, 79, 47, 47, 47, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 47, 201, 201, 201, 201, 201, 201, 201, 201, 79, 47, 47, 47, 47, 10, 6, 6, 4, 4, 47, 47, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 414 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114042 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114042/1 /scratch/stefan/7770410/working/building/REAL300020114042 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1703) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1703 `/scratch/stefan/7770410/working/3D/1703' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CC1=O) `REAL300020114042.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114042 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 29, 44, 48, 48, 48, 48, 9, 9, 1, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 9, 29, 29, 44, 44, 1, 1, 17, 17] 201 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44]) total number of confs: 220 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114042 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 27, 27, 27, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 73, 73, 73, 73, 73, 73, 73, 73, 27, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 73, 73] 201 rigid atoms, others: [36, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 169 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114042 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 73, 73, 73, 140, 201, 201, 201, 201, 201, 73, 73, 17, 1, 1, 1, 1, 2, 2, 2, 1, 5, 17, 17, 17, 17, 73, 140, 140, 201, 201, 17, 17, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 43, 44, 23, 24, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 840 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114042 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 80, 80, 80, 48, 48, 48, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 48, 201, 201, 201, 201, 201, 201, 201, 201, 80, 48, 48, 48, 48, 10, 6, 6, 4, 4, 48, 48, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 417 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114042 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114042 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114042/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114042/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114042 Building REAL300020114043 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114043' /scratch/stefan/7770410/working/building/REAL300020114043 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114043 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114043/0 /scratch/stefan/7770410/working/building/REAL300020114043 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1704) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1704 `/scratch/stefan/7770410/working/3D/1704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114043.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114043 none COCC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 58, 33, 33, 33, 11, 33, 33, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 19, 27, 31, 31, 31, 31, 5, 5, 1, 74, 74, 74, 58, 58, 33, 25, 33, 33, 6, 1, 1, 1, 1, 5, 19, 19, 27, 27, 1, 1] 201 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 375 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114043 none COCC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [122, 105, 73, 73, 73, 35, 73, 73, 19, 19, 19, 5, 5, 5, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 5, 122, 122, 122, 105, 105, 73, 55, 73, 73, 19, 5, 5, 5, 5, 1, 7, 7, 9, 9, 5, 5] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 484 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114043 none COCC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 33, 33, 33, 73, 73, 73, 126, 156, 159, 159, 159, 159, 73, 73, 33, 16, 16, 16, 7, 7, 1, 1, 1, 1, 9, 33, 33, 33, 33, 73, 126, 126, 156, 156, 33, 33] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 36] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 619 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114043 none COCC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 162, 162, 162, 110, 162, 162, 68, 68, 68, 36, 36, 36, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 36, 201, 201, 201, 201, 201, 162, 141, 162, 162, 68, 36, 36, 36, 36, 14, 6, 6, 4, 4, 36, 36] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 762 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114043 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114043/1 /scratch/stefan/7770410/working/building/REAL300020114043 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1705) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1705 `/scratch/stefan/7770410/working/3D/1705' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114043.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114043/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114043 none COCC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 58, 33, 33, 33, 11, 33, 33, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 19, 27, 31, 31, 31, 31, 5, 5, 1, 74, 74, 74, 58, 58, 33, 25, 33, 33, 6, 1, 1, 1, 1, 5, 19, 19, 27, 27, 1, 1] 201 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 375 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114043 none COCC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [122, 105, 73, 73, 73, 35, 73, 73, 19, 19, 19, 5, 5, 5, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 5, 122, 122, 122, 105, 105, 73, 55, 73, 73, 19, 5, 5, 5, 5, 1, 7, 7, 9, 9, 5, 5] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 484 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114043 none COCC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 33, 33, 33, 73, 73, 73, 126, 156, 159, 159, 159, 159, 73, 73, 33, 16, 16, 16, 7, 7, 1, 1, 1, 1, 9, 33, 33, 33, 33, 73, 126, 126, 156, 156, 33, 33] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 36] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 619 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114043 none COCC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 161, 161, 161, 109, 161, 161, 66, 66, 66, 35, 35, 35, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 35, 201, 201, 201, 201, 201, 161, 138, 161, 161, 66, 35, 35, 35, 35, 13, 6, 6, 4, 4, 35, 35] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 765 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114043 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114043 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114043/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114043/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114043 Building REAL300020114044 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114044' /scratch/stefan/7770410/working/building/REAL300020114044 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114044 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114044/0 /scratch/stefan/7770410/working/building/REAL300020114044 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1706) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1706 `/scratch/stefan/7770410/working/3D/1706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=NN1C) `REAL300020114044.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114044 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [38, 24, 24, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 24, 33, 41, 41, 41, 41, 6, 6, 1, 24, 24, 24, 24, 38, 38, 38, 38, 38, 6, 1, 1, 1, 1, 6, 24, 24, 33, 33, 1, 1, 24, 24, 24, 24] 138 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 262 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114044 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [78, 48, 48, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 7, 9, 12, 12, 12, 12, 1, 1, 6, 48, 48, 48, 48, 78, 78, 78, 78, 78, 22, 6, 6, 6, 6, 1, 7, 7, 9, 9, 6, 6, 48, 48, 48, 48] 138 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 314 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114044 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 9, 9, 9, 24, 24, 24, 48, 48, 48, 79, 87, 87, 87, 87, 87, 48, 48, 24, 1, 1, 1, 1, 3, 3, 3, 2, 2, 9, 24, 24, 24, 24, 48, 79, 79, 87, 87, 24, 24, 1, 2, 2, 2] 138 rigid atoms, others: [1, 2, 3, 4, 44, 23, 24, 25, 26] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 308 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114044 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [138, 87, 87, 69, 69, 69, 44, 44, 44, 15, 15, 15, 7, 4, 1, 1, 1, 1, 1, 1, 15, 15, 44, 87, 87, 87, 87, 138, 138, 138, 138, 138, 69, 44, 44, 44, 44, 15, 7, 7, 4, 4, 44, 44, 87, 87, 87, 87] 138 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 538 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114044 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114044/1 /scratch/stefan/7770410/working/building/REAL300020114044 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1707) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1707 `/scratch/stefan/7770410/working/3D/1707' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=NN1C) `REAL300020114044.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114044/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114044 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [38, 24, 24, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 24, 33, 41, 41, 41, 41, 6, 6, 1, 24, 24, 24, 24, 38, 38, 38, 38, 38, 6, 1, 1, 1, 1, 6, 24, 24, 33, 33, 1, 1, 24, 24, 24, 24] 138 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 262 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114044 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [78, 48, 48, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 7, 9, 12, 12, 12, 12, 1, 1, 6, 48, 48, 48, 48, 78, 78, 78, 78, 78, 22, 6, 6, 6, 6, 1, 7, 7, 9, 9, 6, 6, 48, 48, 48, 48] 138 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 314 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114044 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 9, 9, 9, 24, 24, 24, 48, 48, 48, 79, 87, 87, 87, 87, 87, 48, 48, 24, 1, 1, 1, 1, 3, 3, 3, 2, 2, 9, 24, 24, 24, 24, 48, 79, 79, 87, 87, 24, 24, 1, 2, 2, 2] 138 rigid atoms, others: [1, 2, 3, 4, 44, 23, 24, 25, 26] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 308 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114044 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [138, 87, 87, 69, 69, 69, 44, 44, 44, 15, 15, 15, 7, 4, 1, 1, 1, 1, 1, 1, 15, 15, 44, 87, 87, 87, 87, 138, 138, 138, 138, 138, 69, 44, 44, 44, 44, 15, 7, 7, 4, 4, 44, 44, 87, 87, 87, 87] 138 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 538 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114044 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114044 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114044/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114044/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114044 Building REAL300020114045 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114045' /scratch/stefan/7770410/working/building/REAL300020114045 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114045 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114045/0 /scratch/stefan/7770410/working/building/REAL300020114045 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1708) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1708 `/scratch/stefan/7770410/working/3D/1708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=NN1C) `REAL300020114045.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114045 none CCCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 43, 29, 29, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 37, 45, 52, 52, 52, 52, 7, 7, 1, 29, 29, 29, 29, 44, 44, 44, 44, 44, 43, 43, 6, 1, 1, 1, 1, 7, 37, 37, 45, 45, 1, 1, 29, 29, 29, 29] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 45, 46, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50]) total number of confs: 308 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114045 none CCCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 72, 72, 22, 22, 22, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 7, 72, 72, 72, 72, 101, 101, 101, 101, 101, 101, 101, 22, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7, 72, 72, 72, 72] 201 rigid atoms, others: [40, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 341 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114045 none CCCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 1, 1, 1, 1, 7, 7, 7, 29, 29, 29, 72, 72, 72, 140, 167, 172, 172, 172, 172, 72, 72, 29, 1, 1, 1, 1, 4, 3, 3, 4, 4, 2, 2, 7, 29, 29, 29, 29, 72, 140, 140, 167, 167, 29, 29, 1, 2, 2, 2] 201 rigid atoms, others: [2, 3, 4, 5, 47, 24, 25, 26, 27] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50]) total number of confs: 628 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114045 none CCCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 173, 173, 99, 99, 99, 56, 56, 56, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 56, 173, 173, 173, 173, 201, 201, 201, 201, 201, 201, 201, 99, 56, 56, 56, 56, 18, 6, 6, 4, 4, 56, 56, 173, 173, 173, 173] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 568 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114045 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114045/1 /scratch/stefan/7770410/working/building/REAL300020114045 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1709) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1709 `/scratch/stefan/7770410/working/3D/1709' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=NN1C) `REAL300020114045.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114045/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114045 none CCCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 43, 29, 29, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 37, 45, 52, 52, 52, 52, 7, 7, 1, 29, 29, 29, 29, 44, 44, 44, 44, 44, 43, 43, 6, 1, 1, 1, 1, 7, 37, 37, 45, 45, 1, 1, 29, 29, 29, 29] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 45, 46, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50]) total number of confs: 308 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114045 none CCCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 72, 72, 22, 22, 22, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 7, 72, 72, 72, 72, 101, 101, 101, 101, 101, 101, 101, 22, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7, 72, 72, 72, 72] 201 rigid atoms, others: [40, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 341 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114045 none CCCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 1, 1, 1, 1, 7, 7, 7, 29, 29, 29, 72, 72, 72, 140, 167, 172, 172, 172, 172, 72, 72, 29, 1, 1, 1, 1, 4, 3, 3, 4, 4, 2, 2, 7, 29, 29, 29, 29, 72, 140, 140, 167, 167, 29, 29, 1, 2, 2, 2] 201 rigid atoms, others: [2, 3, 4, 5, 47, 24, 25, 26, 27] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50]) total number of confs: 628 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114045 none CCCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 173, 173, 99, 99, 99, 56, 56, 56, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 56, 173, 173, 173, 173, 201, 201, 201, 201, 201, 201, 201, 99, 56, 56, 56, 56, 18, 6, 6, 4, 4, 56, 56, 173, 173, 173, 173] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 568 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114045 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114045 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114045/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114045/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114045 Building REAL300020114046 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114046' /scratch/stefan/7770410/working/building/REAL300020114046 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114046 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114046/0 /scratch/stefan/7770410/working/building/REAL300020114046 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1710) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1710 `/scratch/stefan/7770410/working/3D/1710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=C(C(C)C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114046.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114046 none CCN1N=C(C(C)C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 21, 21, 21, 21, 21, 46, 46, 21, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 21, 29, 40, 40, 40, 40, 5, 5, 1, 41, 41, 41, 41, 41, 46, 46, 46, 46, 46, 46, 46, 21, 6, 1, 1, 1, 1, 5, 21, 21, 29, 29, 1, 1] 201 rigid atoms, others: [45, 44, 43, 12, 13, 14, 15, 16, 52, 46, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 393 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114046 none CCN1N=C(C(C)C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 50, 50, 50, 50, 50, 90, 90, 50, 19, 19, 19, 5, 5, 5, 1, 1, 1, 1, 1, 6, 8, 12, 12, 12, 12, 1, 1, 5, 86, 86, 86, 86, 86, 90, 90, 90, 90, 90, 90, 90, 50, 19, 5, 5, 5, 5, 1, 6, 6, 8, 8, 5, 5] 201 rigid atoms, others: [15, 47, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 539 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114046 none CCN1N=C(C(C)C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 6, 6, 6, 21, 21, 21, 50, 50, 50, 100, 121, 135, 135, 135, 135, 50, 50, 21, 6, 6, 6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 1, 6, 21, 21, 21, 21, 50, 100, 100, 121, 121, 21, 21] 201 rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 41] set([0, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 490 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114046 none CCN1N=C(C(C)C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [190, 139, 139, 139, 139, 139, 168, 168, 139, 86, 86, 86, 45, 45, 45, 17, 17, 17, 7, 4, 1, 1, 1, 1, 1, 1, 17, 17, 45, 190, 190, 190, 190, 190, 168, 168, 168, 168, 168, 168, 168, 139, 86, 45, 45, 45, 45, 17, 7, 7, 4, 4, 45, 45] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 829 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114046 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114046/1 /scratch/stefan/7770410/working/building/REAL300020114046 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1711) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1711 `/scratch/stefan/7770410/working/3D/1711' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=C(C(C)C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114046.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114046 none CCN1N=C(C(C)C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 21, 21, 21, 21, 21, 46, 46, 21, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 21, 29, 40, 40, 40, 40, 5, 5, 1, 41, 41, 41, 41, 41, 46, 46, 46, 46, 46, 46, 46, 21, 6, 1, 1, 1, 1, 5, 21, 21, 29, 29, 1, 1] 201 rigid atoms, others: [45, 44, 43, 12, 13, 14, 15, 16, 52, 46, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 393 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114046 none CCN1N=C(C(C)C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 50, 50, 50, 50, 50, 90, 90, 50, 19, 19, 19, 5, 5, 5, 1, 1, 1, 1, 1, 6, 8, 12, 12, 12, 12, 1, 1, 5, 86, 86, 86, 86, 86, 90, 90, 90, 90, 90, 90, 90, 50, 19, 5, 5, 5, 5, 1, 6, 6, 8, 8, 5, 5] 201 rigid atoms, others: [15, 47, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 539 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114046 none CCN1N=C(C(C)C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 6, 6, 6, 21, 21, 21, 50, 50, 50, 100, 121, 135, 135, 135, 135, 50, 50, 21, 6, 6, 6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 1, 6, 21, 21, 21, 21, 50, 100, 100, 121, 121, 21, 21] 201 rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 41] set([0, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 490 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114046 none CCN1N=C(C(C)C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [190, 138, 138, 138, 138, 138, 168, 168, 138, 85, 85, 85, 44, 44, 44, 16, 16, 16, 7, 4, 1, 1, 1, 1, 1, 1, 16, 16, 44, 190, 190, 190, 190, 190, 168, 168, 168, 168, 168, 168, 168, 138, 85, 44, 44, 44, 44, 16, 7, 7, 4, 4, 44, 44] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 840 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114046 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114046 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114046/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114046/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114046 Building REAL300020114047 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114047' /scratch/stefan/7770410/working/building/REAL300020114047 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114047 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114047/0 /scratch/stefan/7770410/working/building/REAL300020114047 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1712) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1712 `/scratch/stefan/7770410/working/3D/1712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC2=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)NN=C2C=C1) `REAL300020114047.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114047 none CC1=CC2=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)NN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 46, 64, 76, 76, 76, 76, 12, 12, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 12, 46, 46, 64, 64, 1, 1, 18, 18, 18] 201 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 303 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114047 none CC1=CC2=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)NN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 87, 39, 39, 39, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 12, 87, 87, 87, 87, 87, 87, 87, 87, 87, 39, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 87, 87, 87] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 221 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114047 none CC1=CC2=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)NN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 87, 87, 87, 162, 201, 201, 201, 201, 201, 87, 87, 18, 1, 1, 1, 1, 1, 2, 2, 2, 1, 5, 18, 18, 18, 18, 87, 162, 162, 201, 201, 18, 18, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 45, 46, 47, 24, 25, 26, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 757 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114047 none CC1=CC2=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)NN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 138, 138, 138, 77, 77, 77, 16, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 77, 201, 201, 201, 201, 201, 201, 201, 201, 201, 138, 77, 77, 77, 77, 16, 6, 6, 4, 4, 77, 77, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 499 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114047 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114047/1 /scratch/stefan/7770410/working/building/REAL300020114047 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1713) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1713 `/scratch/stefan/7770410/working/3D/1713' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC2=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)NN=C2C=C1) `REAL300020114047.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114047/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114047 none CC1=CC2=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)NN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 48, 66, 77, 77, 77, 77, 12, 12, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 12, 48, 48, 66, 66, 1, 1, 18, 18, 18] 201 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 310 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114047 none CC1=CC2=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)NN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 86, 40, 40, 40, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 12, 86, 86, 86, 86, 86, 86, 86, 86, 86, 40, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 86, 86, 86] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 220 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114047 none CC1=CC2=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)NN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 86, 86, 86, 160, 201, 201, 201, 201, 201, 86, 86, 18, 1, 1, 1, 1, 1, 2, 2, 2, 1, 6, 18, 18, 18, 18, 86, 160, 160, 201, 201, 18, 18, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 45, 46, 47, 24, 25, 26, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 757 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114047 none CC1=CC2=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)NN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 138, 138, 138, 79, 79, 79, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 79, 201, 201, 201, 201, 201, 201, 201, 201, 201, 138, 79, 79, 79, 79, 17, 6, 6, 4, 4, 79, 79, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 494 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114047 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114047 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114047/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114047/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114047 Building REAL300020114048 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114048' /scratch/stefan/7770410/working/building/REAL300020114048 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114048 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114048/0 /scratch/stefan/7770410/working/building/REAL300020114048 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1714) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1714 `/scratch/stefan/7770410/working/3D/1714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1CCCNC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114048.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114048 none O=C(CN1CCCNC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 29, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 9, 9, 9, 33, 46, 52, 52, 52, 52, 9, 9, 1, 29, 29, 33, 33, 33, 33, 33, 33, 33, 6, 1, 1, 1, 1, 9, 33, 33, 46, 46, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 300 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114048 none O=C(CN1CCCNC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 107, 111, 111, 111, 111, 111, 111, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 107, 107, 111, 111, 111, 111, 111, 111, 111, 30, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 413 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114048 none O=C(CN1CCCNC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 3, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 33, 33, 33, 111, 111, 111, 182, 201, 201, 201, 201, 201, 111, 111, 33, 3, 3, 1, 1, 1, 1, 1, 1, 1, 13, 33, 33, 33, 33, 111, 182, 182, 201, 201, 33, 33] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 667 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114048 none O=C(CN1CCCNC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 201, 201, 201, 201, 201, 201, 201, 53, 53, 53, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 53, 201, 201, 201, 201, 201, 201, 201, 201, 201, 105, 53, 53, 53, 53, 12, 6, 6, 4, 4, 53, 53] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 727 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114048 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114048/1 /scratch/stefan/7770410/working/building/REAL300020114048 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1715) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1715 `/scratch/stefan/7770410/working/3D/1715' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1CCCNC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114048.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114048/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114048 none O=C(CN1CCCNC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 29, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 9, 9, 9, 33, 46, 52, 52, 52, 52, 9, 9, 1, 29, 29, 33, 33, 33, 33, 33, 33, 33, 6, 1, 1, 1, 1, 9, 33, 33, 46, 46, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 300 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114048 none O=C(CN1CCCNC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 107, 111, 111, 111, 111, 111, 111, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 107, 107, 111, 111, 111, 111, 111, 111, 111, 30, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 413 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114048 none O=C(CN1CCCNC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 3, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 33, 33, 33, 111, 111, 111, 182, 201, 201, 201, 201, 201, 111, 111, 33, 3, 3, 1, 1, 1, 1, 1, 1, 1, 13, 33, 33, 33, 33, 111, 182, 182, 201, 201, 33, 33] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 667 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114048 none O=C(CN1CCCNC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 201, 201, 201, 201, 201, 201, 201, 52, 52, 52, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 52, 201, 201, 201, 201, 201, 201, 201, 201, 201, 104, 52, 52, 52, 52, 11, 6, 6, 4, 4, 52, 52] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 732 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114048 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114048 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114048/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114048/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114048 Building REAL300020114049 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114049' /scratch/stefan/7770410/working/building/REAL300020114049 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114049 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114049/0 /scratch/stefan/7770410/working/building/REAL300020114049 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1716) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1716 `/scratch/stefan/7770410/working/3D/1716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114049.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114049 none O=C(NC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 9, 9, 22, 22, 22, 22, 22, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 55, 73, 92, 92, 92, 92, 11, 11, 1, 10, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 55, 55, 73, 73, 1, 1] 201 rigid atoms, others: [45, 35, 36, 37, 38, 44, 11, 12, 13, 14, 15, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 367 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114049 none O=C(NC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 46, 52, 52, 98, 98, 98, 98, 98, 46, 46, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 11, 52, 98, 98, 98, 98, 98, 46, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11] 201 rigid atoms, others: [39, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 260 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114049 none O=C(NC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 22, 22, 22, 98, 98, 98, 172, 201, 201, 201, 201, 201, 98, 98, 22, 5, 1, 1, 1, 1, 1, 9, 22, 22, 22, 22, 98, 172, 172, 201, 201, 22, 22] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 694 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114049 none O=C(NC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [186, 180, 186, 186, 201, 201, 201, 201, 201, 180, 180, 93, 93, 93, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 93, 186, 201, 201, 201, 201, 201, 180, 93, 93, 93, 93, 17, 6, 6, 4, 4, 93, 93] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 547 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114049 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114049/1 /scratch/stefan/7770410/working/building/REAL300020114049 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1717) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1717 `/scratch/stefan/7770410/working/3D/1717' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114049.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114049 none O=C(NC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 9, 9, 22, 22, 22, 22, 22, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 55, 73, 92, 92, 92, 92, 11, 11, 1, 10, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 55, 55, 73, 73, 1, 1] 201 rigid atoms, others: [45, 35, 36, 37, 38, 44, 11, 12, 13, 14, 15, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 367 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114049 none O=C(NC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 46, 52, 52, 99, 99, 99, 99, 99, 46, 46, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 11, 52, 99, 99, 99, 99, 99, 46, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11] 201 rigid atoms, others: [39, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 262 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114049 none O=C(NC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 22, 22, 22, 99, 99, 99, 172, 201, 201, 201, 201, 201, 99, 99, 22, 5, 1, 1, 1, 1, 1, 9, 22, 22, 22, 22, 99, 172, 172, 201, 201, 22, 22] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 689 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114049 none O=C(NC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [186, 180, 186, 186, 201, 201, 201, 201, 201, 180, 180, 93, 93, 93, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 93, 186, 201, 201, 201, 201, 201, 180, 93, 93, 93, 93, 17, 6, 6, 4, 4, 93, 93] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 549 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114049 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114049 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114049/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114049/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114049 Building REAL300020114050 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114050' /scratch/stefan/7770410/working/building/REAL300020114050 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114050 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114050/0 /scratch/stefan/7770410/working/building/REAL300020114050 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1718) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1718 `/scratch/stefan/7770410/working/3D/1718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN2C=CC=NC2=N1) `REAL300020114050.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114050 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN2C=CC=NC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 13, 56, 84, 84, 84, 84, 84, 84, 84, 84, 56, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13, 84, 84, 84, 84] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 237 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114050 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN2C=CC=NC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 100, 100, 100, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 100, 200, 201, 201, 201, 201, 201, 201, 201, 201, 200, 100, 100, 100, 100, 15, 6, 6, 4, 4, 100, 100, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 553 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114050 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN2C=CC=NC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 60, 82, 100, 100, 100, 100, 13, 13, 1, 6, 14, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 13, 60, 60, 82, 82, 1, 1, 14, 14, 14, 14] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 381 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114050 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN2C=CC=NC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 14, 14, 14, 84, 84, 84, 160, 201, 201, 201, 201, 201, 84, 84, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 14, 14, 14, 14, 84, 160, 160, 201, 201, 14, 14, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 741 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114050 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114050/1 /scratch/stefan/7770410/working/building/REAL300020114050 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1719) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1719 `/scratch/stefan/7770410/working/3D/1719' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN2C=CC=NC2=N1) `REAL300020114050.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114050/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114050 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN2C=CC=NC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 13, 56, 84, 84, 84, 84, 84, 84, 84, 84, 56, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13, 84, 84, 84, 84] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 237 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114050 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN2C=CC=NC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 100, 100, 100, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 100, 200, 201, 201, 201, 201, 201, 201, 201, 201, 200, 100, 100, 100, 100, 15, 6, 6, 4, 4, 100, 100, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 553 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114050 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN2C=CC=NC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 60, 82, 100, 100, 100, 100, 13, 13, 1, 6, 14, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 13, 60, 60, 82, 82, 1, 1, 14, 14, 14, 14] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 381 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114050 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN2C=CC=NC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 14, 14, 14, 84, 84, 84, 160, 201, 201, 201, 201, 201, 84, 84, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 14, 14, 14, 14, 84, 160, 160, 201, 201, 14, 14, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 741 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114050 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114050 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114050/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114050/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114050 Building REAL300020114051 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114051' /scratch/stefan/7770410/working/building/REAL300020114051 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300020114051 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114051/0 /scratch/stefan/7770410/working/building/REAL300020114051 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1720) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1720 `/scratch/stefan/7770410/working/3D/1720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C12CCC[NH+]1CCC2) `REAL300020114051.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114051 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C12CCC[NH+]1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 9, 9, 9, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 9, 32, 56, 56, 56, 56, 56, 56, 56, 56, 32, 9, 9, 9, 9, 1, 3, 3, 3, 3, 9, 9, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56] 56 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 133 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114051 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C12CCC[NH+]1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 11, 11, 11, 5, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 5, 5, 11, 35, 56, 56, 56, 56, 56, 56, 56, 56, 35, 11, 11, 11, 11, 5, 5, 5, 2, 2, 11, 11, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56] 56 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 143 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114051 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C12CCC[NH+]1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 6, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 56 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 40 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114051 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C12CCC[NH+]1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 19, 19, 19, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 19, 19, 19, 19, 56, 56, 56, 56, 56, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 56 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 27, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 102 number of broken/clashed sets: 5 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114051 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114051 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 0: /scratch/stefan/7770410/working/building/REAL300020114051/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114051 Building REAL300020114052 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114052' /scratch/stefan/7770410/working/building/REAL300020114052 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114052 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114052/0 /scratch/stefan/7770410/working/building/REAL300020114052 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1721) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1721 `/scratch/stefan/7770410/working/3D/1721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)NCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114052.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114052 none CC(C)CC(=O)NCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 117, 117, 75, 75, 75, 75, 62, 18, 18, 18, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 117, 117, 117, 117, 117, 117, 117, 117, 117, 75, 75, 75, 62, 62, 18, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7] 201 rigid atoms, others: [14, 47, 16, 17, 18, 25, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 574 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114052 none CC(C)CC(=O)NCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 150, 150, 150, 150, 138, 50, 50, 50, 34, 34, 34, 10, 10, 10, 5, 2, 1, 1, 1, 1, 1, 1, 10, 10, 34, 201, 201, 201, 201, 201, 201, 201, 201, 201, 150, 150, 150, 138, 138, 50, 34, 34, 34, 34, 10, 5, 5, 2, 2, 34, 34] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 883 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114052 none CC(C)CC(=O)NCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 25, 25, 25, 25, 20, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 20, 32, 32, 32, 32, 32, 7, 7, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43, 25, 25, 25, 20, 20, 5, 1, 1, 1, 1, 7, 20, 20, 32, 32, 1, 1] 201 rigid atoms, others: [11, 15, 44, 43, 12, 13, 14, 45, 52, 46, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 336 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114052 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114052/1 /scratch/stefan/7770410/working/building/REAL300020114052 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1722) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1722 `/scratch/stefan/7770410/working/3D/1722' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)NCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114052.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114052/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114052 none CC(C)CC(=O)NCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 117, 117, 75, 75, 75, 75, 62, 18, 18, 18, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 117, 117, 117, 117, 117, 117, 117, 117, 117, 75, 75, 75, 62, 62, 18, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7] 201 rigid atoms, others: [14, 47, 16, 17, 18, 25, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 574 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114052 none CC(C)CC(=O)NCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 149, 149, 149, 149, 137, 47, 47, 47, 32, 32, 32, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 32, 201, 201, 201, 201, 201, 201, 201, 201, 201, 149, 149, 149, 137, 137, 47, 32, 32, 32, 32, 8, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 883 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114052 none CC(C)CC(=O)NCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 25, 25, 25, 25, 20, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 20, 32, 32, 32, 32, 32, 7, 7, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43, 25, 25, 25, 20, 20, 5, 1, 1, 1, 1, 7, 20, 20, 32, 32, 1, 1] 201 rigid atoms, others: [11, 15, 44, 43, 12, 13, 14, 45, 52, 46, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 336 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114052 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114052 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114052/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114052/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114052 Building REAL300020114053 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114053' /scratch/stefan/7770410/working/building/REAL300020114053 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114053 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114053/0 /scratch/stefan/7770410/working/building/REAL300020114053 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1723) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1723 `/scratch/stefan/7770410/working/3D/1723' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C(F)(F)F)CCCC1) `REAL300020114053.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114053 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C(F)(F)F)CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 15, 15, 15, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 10, 44, 77, 77, 77, 77, 77, 77, 77, 77, 44, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 77, 77, 77, 77, 77, 77, 77, 77] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 273 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114053 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C(F)(F)F)CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 15, 15, 15, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 56, 56, 56, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 56, 164, 201, 201, 201, 201, 201, 201, 201, 201, 164, 56, 56, 56, 56, 11, 6, 6, 4, 4, 56, 56, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 593 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114053 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C(F)(F)F)CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 15, 15, 15, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 36, 51, 57, 57, 57, 57, 10, 10, 1, 6, 11, 11, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 10, 36, 36, 51, 51, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114053 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C(F)(F)F)CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 15, 15, 15, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 11, 11, 11, 77, 77, 77, 160, 201, 201, 201, 201, 201, 77, 77, 11, 1, 1, 2, 2, 2, 1, 1, 1, 1, 3, 11, 11, 11, 11, 77, 160, 160, 201, 201, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 19, 20, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 790 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114053 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114053/1 /scratch/stefan/7770410/working/building/REAL300020114053 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1724) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1724 `/scratch/stefan/7770410/working/3D/1724' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C(F)(F)F)CCCC1) `REAL300020114053.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114053/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114053 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C(F)(F)F)CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 15, 15, 15, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 11, 11, 11, 11, 1, 1, 10, 44, 76, 76, 76, 76, 76, 76, 76, 76, 44, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 76, 76, 76, 76, 76, 76, 76, 76] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 271 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114053 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C(F)(F)F)CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 15, 15, 15, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 163, 55, 55, 55, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 55, 163, 201, 201, 201, 201, 201, 201, 201, 201, 163, 55, 55, 55, 55, 11, 6, 6, 4, 4, 55, 55, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 595 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114053 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C(F)(F)F)CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 15, 15, 15, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 34, 49, 55, 55, 55, 55, 10, 10, 1, 6, 11, 11, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 10, 34, 34, 49, 49, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114053 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C(F)(F)F)CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 15, 15, 15, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 11, 11, 11, 76, 76, 76, 160, 201, 201, 201, 201, 201, 76, 76, 11, 1, 1, 2, 2, 2, 1, 1, 1, 1, 3, 11, 11, 11, 11, 76, 160, 160, 201, 201, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 19, 20, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 798 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114053 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114053 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114053/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114053/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114053 Building REAL300020114054 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114054' /scratch/stefan/7770410/working/building/REAL300020114054 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114054 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114054/0 /scratch/stefan/7770410/working/building/REAL300020114054 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1725) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1725 `/scratch/stefan/7770410/working/3D/1725' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(F)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114054.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114054 none CC1=CC=CC(F)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 8, 23, 23, 23, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 36, 51, 59, 59, 59, 59, 11, 11, 1, 23, 23, 23, 23, 23, 23, 5, 1, 1, 1, 1, 11, 36, 36, 51, 51, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 44, 10, 11, 12, 13, 14, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 297 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114054 none CC1=CC=CC(F)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 50, 107, 107, 107, 35, 35, 35, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 107, 107, 107, 107, 107, 107, 35, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11] 201 rigid atoms, others: [38, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 397 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114054 none CC1=CC=CC(F)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 23, 23, 23, 107, 107, 107, 169, 201, 201, 201, 201, 201, 107, 107, 23, 2, 2, 2, 1, 1, 1, 9, 23, 23, 23, 23, 107, 169, 169, 201, 201, 23, 23] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 695 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114054 none CC1=CC=CC(F)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 169, 201, 201, 201, 120, 120, 120, 61, 61, 61, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 61, 201, 201, 201, 201, 201, 201, 120, 61, 61, 61, 61, 12, 6, 6, 4, 4, 61, 61] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 611 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114054 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114054/1 /scratch/stefan/7770410/working/building/REAL300020114054 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1726) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1726 `/scratch/stefan/7770410/working/3D/1726' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(F)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114054.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114054 none CC1=CC=CC(F)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 8, 24, 24, 24, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 36, 51, 59, 59, 59, 59, 11, 11, 1, 24, 24, 24, 24, 24, 24, 5, 1, 1, 1, 1, 11, 36, 36, 51, 51, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 44, 10, 11, 12, 13, 14, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 303 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114054 none CC1=CC=CC(F)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 53, 108, 108, 108, 35, 35, 35, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 108, 108, 108, 108, 108, 108, 35, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11] 201 rigid atoms, others: [38, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 401 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114054 none CC1=CC=CC(F)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 24, 24, 24, 108, 108, 108, 169, 201, 201, 201, 201, 201, 108, 108, 24, 2, 2, 2, 1, 1, 1, 9, 24, 24, 24, 24, 108, 169, 169, 201, 201, 24, 24] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 691 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114054 none CC1=CC=CC(F)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 161, 201, 201, 201, 119, 119, 119, 60, 60, 60, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 60, 201, 201, 201, 201, 201, 201, 119, 60, 60, 60, 60, 12, 6, 6, 4, 4, 60, 60] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 650 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114054 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114054 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114054/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114054/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114054 Building REAL300020114055 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114055' /scratch/stefan/7770410/working/building/REAL300020114055 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114055 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114055/0 /scratch/stefan/7770410/working/building/REAL300020114055 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1727) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1727 `/scratch/stefan/7770410/working/3D/1727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1C(C)(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114055.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114055 none CC1=CC=CC=C1C(C)(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 19, 22, 22, 19, 6, 19, 19, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 34, 48, 51, 51, 51, 51, 11, 11, 1, 22, 22, 22, 22, 19, 22, 22, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 11, 34, 34, 48, 48, 1, 1] 201 rigid atoms, others: [45, 44, 43, 12, 13, 14, 15, 16, 52, 46, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 276 number of broken/clashed sets: 194 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114055 none CC1=CC=CC=C1C(C)(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 96, 99, 99, 96, 39, 96, 96, 39, 39, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 99, 99, 99, 99, 96, 99, 99, 96, 96, 96, 96, 96, 96, 39, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11] 201 rigid atoms, others: [15, 47, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 408 number of broken/clashed sets: 194 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114055 none CC1=CC=CC=C1C(C)(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 22, 22, 22, 99, 99, 99, 169, 201, 201, 201, 201, 201, 99, 99, 22, 2, 2, 2, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 22, 22, 22, 22, 99, 169, 169, 201, 201, 22, 22] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 34, 35, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 736 number of broken/clashed sets: 194 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114055 none CC1=CC=CC=C1C(C)(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 125, 201, 201, 125, 125, 53, 53, 53, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 53, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 125, 53, 53, 53, 53, 12, 6, 6, 4, 4, 53, 53] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 757 number of broken/clashed sets: 194 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114055 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114055/1 /scratch/stefan/7770410/working/building/REAL300020114055 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1728) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1728 `/scratch/stefan/7770410/working/3D/1728' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1C(C)(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114055.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114055 none CC1=CC=CC=C1C(C)(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 19, 22, 22, 19, 6, 19, 19, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 34, 48, 51, 51, 51, 51, 11, 11, 1, 22, 22, 22, 22, 19, 22, 22, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 11, 34, 34, 48, 48, 1, 1] 201 rigid atoms, others: [45, 44, 43, 12, 13, 14, 15, 16, 52, 46, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 276 number of broken/clashed sets: 194 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114055 none CC1=CC=CC=C1C(C)(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 96, 99, 99, 96, 39, 96, 96, 39, 39, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 99, 99, 99, 99, 96, 99, 99, 96, 96, 96, 96, 96, 96, 39, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11] 201 rigid atoms, others: [15, 47, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 408 number of broken/clashed sets: 194 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114055 none CC1=CC=CC=C1C(C)(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 22, 22, 22, 99, 99, 99, 169, 201, 201, 201, 201, 201, 99, 99, 22, 2, 2, 2, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 22, 22, 22, 22, 99, 169, 169, 201, 201, 22, 22] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 34, 35, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 736 number of broken/clashed sets: 194 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114055 none CC1=CC=CC=C1C(C)(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 125, 201, 201, 125, 125, 52, 52, 52, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 52, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 125, 52, 52, 52, 52, 12, 6, 6, 4, 4, 52, 52] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 755 number of broken/clashed sets: 194 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114055 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114055 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114055/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114055/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114055 Building REAL300020114056 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114056' /scratch/stefan/7770410/working/building/REAL300020114056 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114056 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114056/0 /scratch/stefan/7770410/working/building/REAL300020114056 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1729) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1729 `/scratch/stefan/7770410/working/3D/1729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C(C)=C1C(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114056.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114056 none CC1=NN(C)C(C)=C1C(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 11, 6, 11, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 36, 51, 59, 59, 59, 59, 11, 11, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 11, 11, 11, 6, 1, 1, 1, 1, 11, 36, 36, 51, 51, 1, 1] 201 rigid atoms, others: [45, 44, 43, 12, 13, 14, 15, 16, 52, 46, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 281 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114056 none CC1=NN(C)C(C)=C1C(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 94, 94, 94, 94, 60, 38, 60, 38, 38, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 11, 94, 94, 94, 94, 94, 94, 94, 94, 94, 60, 60, 60, 60, 38, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11] 201 rigid atoms, others: [15, 47, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 338 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114056 none CC1=NN(C)C(C)=C1C(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 21, 21, 21, 94, 94, 94, 169, 201, 201, 201, 201, 201, 94, 94, 21, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 6, 21, 21, 21, 21, 94, 169, 169, 201, 201, 21, 21] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 754 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114056 none CC1=NN(C)C(C)=C1C(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 144, 120, 144, 120, 120, 60, 60, 60, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 60, 201, 201, 201, 201, 201, 201, 201, 201, 201, 144, 144, 144, 144, 120, 60, 60, 60, 60, 14, 6, 6, 4, 4, 60, 60] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 585 number of broken/clashed sets: 200 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114056 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114056/1 /scratch/stefan/7770410/working/building/REAL300020114056 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1730) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1730 `/scratch/stefan/7770410/working/3D/1730' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C(C)=C1C(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114056.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114056 none CC1=NN(C)C(C)=C1C(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 11, 6, 11, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 36, 51, 59, 59, 59, 59, 11, 11, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 11, 11, 11, 6, 1, 1, 1, 1, 11, 36, 36, 51, 51, 1, 1] 201 rigid atoms, others: [45, 44, 43, 12, 13, 14, 15, 16, 52, 46, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 281 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114056 none CC1=NN(C)C(C)=C1C(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 94, 94, 94, 94, 60, 38, 60, 38, 38, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 11, 94, 94, 94, 94, 94, 94, 94, 94, 94, 60, 60, 60, 60, 38, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11] 201 rigid atoms, others: [15, 47, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 338 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114056 none CC1=NN(C)C(C)=C1C(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 21, 21, 21, 94, 94, 94, 169, 201, 201, 201, 201, 201, 94, 94, 21, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 6, 21, 21, 21, 21, 94, 169, 169, 201, 201, 21, 21] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 754 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114056 none CC1=NN(C)C(C)=C1C(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 144, 120, 144, 120, 120, 60, 60, 60, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 60, 201, 201, 201, 201, 201, 201, 201, 201, 201, 144, 144, 144, 144, 120, 60, 60, 60, 60, 14, 6, 6, 4, 4, 60, 60] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 585 number of broken/clashed sets: 200 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114056 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114056 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114056/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114056/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114056 Building REAL300020114057 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114057' /scratch/stefan/7770410/working/building/REAL300020114057 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114057 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114057/0 /scratch/stefan/7770410/working/building/REAL300020114057 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1731) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1731 `/scratch/stefan/7770410/working/3D/1731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COCC1CCCO1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114057.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114057 none O=C(COCC1CCCO1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 17, 30, 41, 51, 51, 51, 51, 1, 1, 1, 1, 1, 9, 9, 9, 20, 31, 31, 31, 31, 31, 9, 9, 1, 17, 17, 41, 41, 51, 51, 51, 51, 51, 51, 51, 6, 1, 1, 1, 1, 9, 20, 20, 31, 31, 1, 1] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 304 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114057 none O=C(COCC1CCCO1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 71, 81, 103, 129, 129, 129, 129, 9, 9, 9, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 9, 71, 71, 103, 103, 129, 129, 129, 129, 129, 129, 129, 30, 9, 9, 9, 9, 1, 5, 5, 7, 7, 9, 9] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 541 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114057 none O=C(COCC1CCCO1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 20, 12, 7, 1, 1, 1, 1, 1, 1, 24, 24, 51, 51, 51, 129, 129, 129, 178, 201, 201, 201, 201, 201, 129, 129, 51, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 24, 51, 51, 51, 51, 129, 178, 178, 201, 201, 51, 51] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 36, 37, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 666 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114057 none O=C(COCC1CCCO1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 127, 145, 169, 201, 201, 201, 201, 31, 31, 31, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 31, 127, 127, 169, 169, 201, 201, 201, 201, 201, 201, 201, 71, 31, 31, 31, 31, 7, 4, 4, 2, 2, 31, 31] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 791 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114057 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114057/1 /scratch/stefan/7770410/working/building/REAL300020114057 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1732) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1732 `/scratch/stefan/7770410/working/3D/1732' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COCC1CCCO1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114057.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114057 none O=C(COCC1CCCO1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 18, 30, 43, 53, 53, 53, 53, 1, 1, 1, 1, 1, 9, 9, 9, 20, 31, 31, 31, 31, 31, 9, 9, 1, 18, 18, 43, 43, 53, 53, 53, 53, 53, 53, 53, 6, 1, 1, 1, 1, 9, 20, 20, 31, 31, 1, 1] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 317 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114057 none O=C(COCC1CCCO1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 73, 82, 105, 130, 130, 130, 130, 9, 9, 9, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 9, 73, 73, 105, 105, 130, 130, 130, 130, 130, 130, 130, 30, 9, 9, 9, 9, 1, 5, 5, 7, 7, 9, 9] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 547 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114057 none O=C(COCC1CCCO1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 20, 12, 7, 1, 1, 1, 1, 1, 1, 25, 25, 53, 53, 53, 130, 130, 130, 178, 201, 201, 201, 201, 201, 130, 130, 53, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 25, 53, 53, 53, 53, 130, 178, 178, 201, 201, 53, 53] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 36, 37, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 670 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114057 none O=C(COCC1CCCO1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 12, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 128, 146, 169, 201, 201, 201, 201, 30, 30, 30, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 30, 128, 128, 169, 169, 201, 201, 201, 201, 201, 201, 201, 72, 30, 30, 30, 30, 7, 4, 4, 2, 2, 30, 30] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 787 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114057 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114057 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114057/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114057/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114057 Building REAL300020114058 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114058' /scratch/stefan/7770410/working/building/REAL300020114058 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114058 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114058/0 /scratch/stefan/7770410/working/building/REAL300020114058 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1733) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1733 `/scratch/stefan/7770410/working/3D/1733' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(NC(=O)C1CCC1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114058.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114058 none CC(NC(=O)C1CCC1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 14, 14, 14, 14, 37, 37, 37, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 21, 33, 33, 33, 33, 33, 7, 7, 1, 14, 14, 14, 14, 14, 37, 37, 37, 37, 37, 37, 37, 5, 1, 1, 1, 1, 7, 21, 21, 33, 33, 1, 1] 201 rigid atoms, others: [43, 41, 42, 11, 12, 13, 14, 15, 50, 51, 27, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 247 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114058 none CC(NC(=O)C1CCC1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 17, 41, 41, 41, 41, 101, 101, 101, 17, 17, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 41, 41, 41, 41, 41, 101, 101, 101, 101, 101, 101, 101, 17, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7] 201 rigid atoms, others: [45, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 359 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114058 none CC(NC(=O)C1CCC1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 7, 7, 1, 7, 1, 1, 1, 1, 11, 20, 20, 20, 37, 37, 37, 101, 101, 101, 158, 201, 201, 201, 201, 201, 101, 101, 37, 11, 11, 11, 11, 7, 1, 1, 1, 1, 1, 1, 1, 20, 37, 37, 37, 37, 101, 158, 158, 201, 201, 37, 37] 201 rigid atoms, others: [33, 34, 3, 36, 5, 6, 7, 8, 39, 35, 38, 37] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 783 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114058 none CC(NC(=O)C1CCC1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 52, 84, 84, 84, 84, 201, 201, 201, 52, 52, 33, 33, 33, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 33, 84, 84, 84, 84, 84, 201, 201, 201, 201, 201, 201, 201, 52, 33, 33, 33, 33, 8, 4, 4, 2, 2, 33, 33] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 692 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114058 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114058/1 /scratch/stefan/7770410/working/building/REAL300020114058 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1734) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1734 `/scratch/stefan/7770410/working/3D/1734' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(NC(=O)C1CCC1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114058.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114058 none CC(NC(=O)C1CCC1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 14, 14, 14, 14, 37, 37, 37, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 21, 33, 33, 33, 33, 33, 7, 7, 1, 14, 14, 14, 14, 14, 37, 37, 37, 37, 37, 37, 37, 5, 1, 1, 1, 1, 7, 21, 21, 33, 33, 1, 1] 201 rigid atoms, others: [43, 41, 42, 11, 12, 13, 14, 15, 50, 51, 27, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 247 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114058 none CC(NC(=O)C1CCC1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 16, 40, 40, 40, 40, 100, 100, 100, 16, 16, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 40, 40, 40, 40, 40, 100, 100, 100, 100, 100, 100, 100, 16, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7] 201 rigid atoms, others: [45, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 357 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114058 none CC(NC(=O)C1CCC1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 7, 7, 1, 7, 1, 1, 1, 1, 11, 20, 20, 20, 37, 37, 37, 100, 100, 100, 157, 201, 201, 201, 201, 201, 100, 100, 37, 11, 11, 11, 11, 7, 1, 1, 1, 1, 1, 1, 1, 20, 37, 37, 37, 37, 100, 157, 157, 201, 201, 37, 37] 201 rigid atoms, others: [33, 34, 3, 36, 5, 6, 7, 8, 39, 35, 38, 37] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 788 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114058 none CC(NC(=O)C1CCC1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 54, 86, 86, 86, 86, 201, 201, 201, 54, 54, 34, 34, 34, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 34, 86, 86, 86, 86, 86, 201, 201, 201, 201, 201, 201, 201, 54, 34, 34, 34, 34, 9, 4, 4, 2, 2, 34, 34] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 693 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114058 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114058 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114058/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114058/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114058 Building REAL300020114059 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114059' /scratch/stefan/7770410/working/building/REAL300020114059 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114059 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114059/0 /scratch/stefan/7770410/working/building/REAL300020114059 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1735) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1735 `/scratch/stefan/7770410/working/3D/1735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=NC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1) `REAL300020114059.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114059 none CC(C)(C)C1=NC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 14, 28, 28, 11, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 36, 52, 63, 63, 63, 63, 11, 11, 1, 14, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 6, 1, 1, 1, 1, 11, 36, 36, 52, 52, 1, 1, 14] 201 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 49, 50, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 51]) total number of confs: 338 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114059 none CC(C)(C)C1=NC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 72, 114, 114, 69, 72, 72, 40, 40, 40, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 72, 72, 114, 114, 114, 114, 114, 114, 114, 114, 114, 72, 40, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 72] 201 rigid atoms, others: [44, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 453 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114059 none CC(C)(C)C1=NC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 72, 72, 72, 149, 188, 201, 201, 201, 201, 72, 72, 14, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 5, 14, 14, 14, 14, 72, 149, 149, 188, 188, 14, 14, 1] 201 rigid atoms, others: [1, 27, 4, 5, 6, 7, 8, 51, 38, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 728 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114059 none CC(C)(C)C1=NC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 199, 201, 201, 135, 135, 135, 63, 63, 63, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 63, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 135, 63, 63, 63, 63, 12, 6, 6, 4, 4, 63, 63, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 524 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114059 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114059/1 /scratch/stefan/7770410/working/building/REAL300020114059 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1736) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1736 `/scratch/stefan/7770410/working/3D/1736' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=NC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1) `REAL300020114059.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114059/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114059 none CC(C)(C)C1=NC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 14, 28, 28, 11, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 37, 53, 64, 64, 64, 64, 11, 11, 1, 14, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 6, 1, 1, 1, 1, 11, 37, 37, 53, 53, 1, 1, 14] 201 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 49, 50, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 51]) total number of confs: 341 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114059 none CC(C)(C)C1=NC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 71, 114, 114, 68, 71, 71, 39, 39, 39, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 71, 71, 114, 114, 114, 114, 114, 114, 114, 114, 114, 71, 39, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 71] 201 rigid atoms, others: [44, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 457 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114059 none CC(C)(C)C1=NC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 71, 71, 71, 149, 188, 201, 201, 201, 201, 71, 71, 14, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 5, 14, 14, 14, 14, 71, 149, 149, 188, 188, 14, 14, 1] 201 rigid atoms, others: [1, 27, 4, 5, 6, 7, 8, 51, 38, 28] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 730 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114059 none CC(C)(C)C1=NC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 199, 201, 201, 135, 135, 135, 63, 63, 63, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 63, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 135, 63, 63, 63, 63, 12, 6, 6, 4, 4, 63, 63, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 524 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114059 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114059 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114059/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114059/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114059 Building REAL300020114060 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114060' /scratch/stefan/7770410/working/building/REAL300020114060 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114060 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114060/0 /scratch/stefan/7770410/working/building/REAL300020114060 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1737) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1737 `/scratch/stefan/7770410/working/3D/1737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@H](C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(C)(C)C) `REAL300020114060.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114060 none CC(=O)N[C@H](C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 10, 8, 10, 8, 8, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 4, 10, 11, 11, 11, 11, 11, 11, 11, 8, 4, 4, 4, 4, 1, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11] 11 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114060 none CC(=O)N[C@H](C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 10, 9, 10, 9, 9, 6, 6, 6, 5, 5, 5, 4, 2, 1, 1, 1, 1, 1, 1, 5, 5, 6, 10, 11, 11, 11, 11, 11, 11, 11, 9, 6, 6, 6, 6, 5, 4, 4, 2, 2, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11] 11 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 48 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114060 none CC(=O)N[C@H](C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 8, 6, 8, 6, 6, 1, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 5, 5, 5, 4, 4, 1, 8, 9, 9, 9, 10, 10, 10, 10, 6, 1, 1, 1, 1, 4, 5, 5, 5, 5, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9] 11 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114060 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114060/1 /scratch/stefan/7770410/working/building/REAL300020114060 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1738) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1738 `/scratch/stefan/7770410/working/3D/1738' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@H](C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(C)(C)C) `REAL300020114060.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114060/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114060 none CC(=O)N[C@H](C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 10, 8, 10, 8, 8, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 4, 10, 11, 11, 11, 11, 11, 11, 11, 8, 4, 4, 4, 4, 1, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11] 11 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114060 none CC(=O)N[C@H](C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 10, 9, 10, 9, 9, 6, 6, 6, 5, 5, 5, 4, 2, 1, 1, 1, 1, 1, 1, 5, 5, 6, 10, 11, 11, 11, 11, 11, 11, 11, 9, 6, 6, 6, 6, 5, 4, 4, 2, 2, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11] 11 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 48 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114060 none CC(=O)N[C@H](C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 8, 6, 8, 6, 6, 1, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 5, 5, 5, 4, 4, 1, 8, 9, 9, 9, 10, 10, 10, 10, 6, 1, 1, 1, 1, 4, 5, 5, 5, 5, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9] 11 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114060 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114060 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114060/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114060/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114060 Building REAL300020114061 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114061' /scratch/stefan/7770410/working/building/REAL300020114061 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114061 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114061/0 /scratch/stefan/7770410/working/building/REAL300020114061 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1739) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1739 `/scratch/stefan/7770410/working/3D/1739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1C) `REAL300020114061.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114061 none CCC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 9, 9, 9, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 52, 69, 80, 80, 80, 80, 11, 11, 1, 9, 9, 9, 15, 15, 15, 15, 15, 9, 6, 1, 1, 1, 1, 11, 52, 52, 69, 69, 1, 1, 9, 9, 9] 201 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 343 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114061 none CCC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 49, 49, 49, 43, 43, 43, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 11, 49, 49, 49, 85, 85, 85, 85, 85, 49, 43, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 49, 49, 49] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 380 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114061 none CCC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 49, 49, 49, 118, 147, 151, 151, 151, 151, 49, 49, 9, 1, 1, 1, 3, 3, 3, 3, 3, 1, 4, 9, 9, 9, 9, 49, 118, 118, 147, 147, 9, 9, 2, 2, 2] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 24, 25, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 567 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114061 none CCC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 151, 151, 151, 146, 146, 146, 81, 81, 81, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 81, 151, 151, 151, 201, 201, 201, 201, 201, 151, 146, 81, 81, 81, 81, 15, 6, 6, 4, 4, 81, 81, 151, 151, 151] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 716 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114061 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114061/1 /scratch/stefan/7770410/working/building/REAL300020114061 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1740) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1740 `/scratch/stefan/7770410/working/3D/1740' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1C) `REAL300020114061.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114061/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114061 none CCC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 9, 9, 9, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 50, 67, 78, 78, 78, 78, 11, 11, 1, 9, 9, 9, 15, 15, 15, 15, 15, 9, 6, 1, 1, 1, 1, 11, 50, 50, 67, 67, 1, 1, 9, 9, 9] 201 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 337 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114061 none CCC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 49, 49, 49, 43, 43, 43, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 11, 49, 49, 49, 87, 87, 87, 87, 87, 49, 43, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 49, 49, 49] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 392 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114061 none CCC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 49, 49, 49, 115, 144, 149, 149, 149, 149, 49, 49, 9, 1, 1, 1, 3, 3, 3, 3, 3, 1, 4, 9, 9, 9, 9, 49, 115, 115, 144, 144, 9, 9, 2, 2, 2] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 24, 25, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 563 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114061 none CCC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 150, 150, 150, 145, 145, 145, 80, 80, 80, 16, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 80, 150, 150, 150, 201, 201, 201, 201, 201, 150, 145, 80, 80, 80, 80, 16, 6, 6, 4, 4, 80, 80, 150, 150, 150] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 721 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114061 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114061 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114061/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114061/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114061 Building REAL300020114062 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114062' /scratch/stefan/7770410/working/building/REAL300020114062 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114062 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114062/0 /scratch/stefan/7770410/working/building/REAL300020114062 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1741) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1741 `/scratch/stefan/7770410/working/3D/1741' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1) `REAL300020114062.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114062 none CCOC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 31, 14, 14, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 38, 48, 67, 67, 67, 67, 7, 7, 1, 14, 14, 72, 72, 72, 72, 72, 14, 6, 1, 1, 1, 1, 7, 38, 38, 48, 48, 1, 1, 14] 201 rigid atoms, others: [45, 35, 36, 37, 38, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46]) total number of confs: 452 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114062 none CCOC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [136, 89, 49, 49, 49, 49, 29, 29, 29, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 17, 17, 17, 17, 1, 1, 7, 49, 49, 136, 136, 136, 136, 136, 49, 29, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7, 49] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 457 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114062 none CCOC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 49, 49, 49, 126, 146, 177, 177, 177, 177, 49, 49, 14, 1, 1, 15, 15, 15, 14, 14, 1, 5, 14, 14, 14, 14, 49, 126, 126, 146, 146, 14, 14, 1] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 46, 26, 27] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 638 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114062 none CCOC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 179, 179, 179, 179, 169, 169, 169, 72, 72, 72, 20, 20, 20, 6, 4, 1, 1, 1, 1, 1, 1, 20, 20, 72, 179, 179, 201, 201, 201, 201, 201, 179, 169, 72, 72, 72, 72, 20, 6, 6, 4, 4, 72, 72, 179] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 541 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114062 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114062/1 /scratch/stefan/7770410/working/building/REAL300020114062 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1742) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1742 `/scratch/stefan/7770410/working/3D/1742' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1) `REAL300020114062.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114062/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114062 none CCOC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 31, 14, 14, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 38, 48, 67, 67, 67, 67, 7, 7, 1, 14, 14, 72, 72, 72, 72, 72, 14, 6, 1, 1, 1, 1, 7, 38, 38, 48, 48, 1, 1, 14] 201 rigid atoms, others: [45, 35, 36, 37, 38, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46]) total number of confs: 452 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114062 none CCOC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [136, 89, 49, 49, 49, 49, 29, 29, 29, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 17, 17, 17, 17, 1, 1, 7, 49, 49, 136, 136, 136, 136, 136, 49, 29, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7, 49] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 457 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114062 none CCOC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 49, 49, 49, 126, 146, 177, 177, 177, 177, 49, 49, 14, 1, 1, 15, 15, 15, 14, 14, 1, 5, 14, 14, 14, 14, 49, 126, 126, 146, 146, 14, 14, 1] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 46, 26, 27] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 638 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114062 none CCOC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 179, 179, 179, 179, 169, 169, 169, 72, 72, 72, 20, 20, 20, 6, 4, 1, 1, 1, 1, 1, 1, 20, 20, 72, 179, 179, 201, 201, 201, 201, 201, 179, 169, 72, 72, 72, 72, 20, 6, 6, 4, 4, 72, 72, 179] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 541 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114062 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114062 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114062/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114062/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114062 Building REAL300020114063 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114063' /scratch/stefan/7770410/working/building/REAL300020114063 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114063 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114063/0 /scratch/stefan/7770410/working/building/REAL300020114063 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1743) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1743 `/scratch/stefan/7770410/working/3D/1743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=C(C)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1) `REAL300020114063.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114063 none CCN1N=C(C)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 13, 13, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 38, 54, 54, 54, 54, 54, 13, 13, 1, 13, 22, 22, 22, 22, 22, 13, 13, 13, 6, 1, 1, 1, 1, 13, 38, 38, 54, 54, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 284 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114063 none CCN1N=C(C)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 64, 64, 64, 64, 64, 50, 50, 50, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 64, 108, 108, 108, 108, 108, 64, 64, 64, 50, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 429 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114063 none CCN1N=C(C)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 13, 13, 13, 64, 64, 64, 135, 182, 182, 182, 182, 182, 64, 64, 13, 1, 5, 5, 5, 4, 4, 2, 2, 2, 3, 13, 13, 13, 13, 64, 135, 135, 182, 182, 13, 13] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 721 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114063 none CCN1N=C(C)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 183, 183, 183, 183, 183, 167, 167, 167, 53, 53, 53, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 53, 183, 201, 201, 201, 201, 201, 183, 183, 183, 167, 53, 53, 53, 53, 9, 5, 5, 3, 3, 53, 53] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 578 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114063 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114063/1 /scratch/stefan/7770410/working/building/REAL300020114063 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1744) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1744 `/scratch/stefan/7770410/working/3D/1744' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=C(C)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1) `REAL300020114063.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114063/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114063 none CCN1N=C(C)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 13, 13, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 37, 53, 53, 53, 53, 53, 13, 13, 1, 13, 22, 22, 22, 22, 22, 13, 13, 13, 6, 1, 1, 1, 1, 13, 37, 37, 53, 53, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 281 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114063 none CCN1N=C(C)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 64, 64, 64, 64, 64, 50, 50, 50, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 64, 109, 109, 109, 109, 109, 64, 64, 64, 50, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 432 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114063 none CCN1N=C(C)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 13, 13, 13, 64, 64, 64, 134, 182, 182, 182, 182, 182, 64, 64, 13, 1, 5, 5, 5, 4, 4, 2, 2, 2, 3, 13, 13, 13, 13, 64, 134, 134, 182, 182, 13, 13] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 724 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114063 none CCN1N=C(C)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 183, 183, 183, 183, 183, 167, 167, 167, 53, 53, 53, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 53, 183, 201, 201, 201, 201, 201, 183, 183, 183, 167, 53, 53, 53, 53, 9, 5, 5, 3, 3, 53, 53] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 578 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114063 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114063 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114063/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114063/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114063 Building REAL300020114064 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114064' /scratch/stefan/7770410/working/building/REAL300020114064 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114064 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114064/0 /scratch/stefan/7770410/working/building/REAL300020114064 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1745) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1745 `/scratch/stefan/7770410/working/3D/1745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CNC2=CC=C(F)C=C12) `REAL300020114064.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114064 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CNC2=CC=C(F)C=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 7, 7, 7, 1, 1, 1, 1, 1, 8, 13, 18, 18, 18, 18, 1, 1, 7, 29, 82, 82, 82, 82, 82, 82, 82, 82, 82, 29, 7, 7, 7, 7, 1, 8, 8, 13, 13, 7, 7, 82, 82, 82, 82, 82] 165 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 207 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114064 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CNC2=CC=C(F)C=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 63, 63, 63, 24, 24, 24, 7, 4, 1, 1, 1, 1, 1, 1, 24, 24, 63, 113, 165, 165, 165, 165, 165, 165, 165, 165, 165, 113, 63, 63, 63, 63, 24, 7, 7, 4, 4, 63, 63, 165, 165, 165, 165, 165] 165 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 408 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114064 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CNC2=CC=C(F)C=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 32, 43, 58, 58, 58, 58, 7, 7, 1, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 1, 1, 1, 1, 7, 32, 32, 43, 43, 1, 1, 31, 31, 31, 31, 31] 165 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114064 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CNC2=CC=C(F)C=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 31, 31, 31, 82, 82, 82, 148, 165, 165, 165, 165, 165, 82, 82, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 31, 31, 31, 31, 82, 148, 148, 165, 165, 31, 31, 1, 1, 1, 1, 1] 165 rigid atoms, others: [1, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 556 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114064 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114064/1 /scratch/stefan/7770410/working/building/REAL300020114064 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1746) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1746 `/scratch/stefan/7770410/working/3D/1746' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CNC2=CC=C(F)C=C12) `REAL300020114064.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114064 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CNC2=CC=C(F)C=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 7, 7, 7, 1, 1, 1, 1, 1, 8, 13, 18, 18, 18, 18, 1, 1, 7, 29, 82, 82, 82, 82, 82, 82, 82, 82, 82, 29, 7, 7, 7, 7, 1, 8, 8, 13, 13, 7, 7, 82, 82, 82, 82, 82] 162 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 207 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114064 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CNC2=CC=C(F)C=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 62, 62, 62, 25, 25, 25, 7, 4, 1, 1, 1, 1, 1, 1, 25, 25, 62, 112, 162, 162, 162, 162, 162, 162, 162, 162, 162, 112, 62, 62, 62, 62, 25, 7, 7, 4, 4, 62, 62, 162, 162, 162, 162, 162] 162 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 402 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114064 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CNC2=CC=C(F)C=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 31, 42, 56, 56, 56, 56, 7, 7, 1, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 1, 1, 1, 1, 7, 31, 31, 42, 42, 1, 1, 31, 31, 31, 31, 31] 162 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114064 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CNC2=CC=C(F)C=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 31, 31, 31, 82, 82, 82, 146, 162, 162, 162, 162, 162, 82, 82, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 31, 31, 31, 31, 82, 146, 146, 162, 162, 31, 31, 1, 1, 1, 1, 1] 162 rigid atoms, others: [1, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 541 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114064 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114064 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114064/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114064/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114064 Building REAL300020114065 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114065' /scratch/stefan/7770410/working/building/REAL300020114065 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114065 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114065/0 /scratch/stefan/7770410/working/building/REAL300020114065 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1747) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1747 `/scratch/stefan/7770410/working/3D/1747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CN=CC(F)=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114065.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114065 none O=C(CCC1=CN=CC(F)=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 18, 20, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 8, 8, 8, 21, 33, 33, 33, 33, 33, 8, 8, 1, 18, 18, 20, 20, 38, 38, 38, 5, 1, 1, 1, 1, 8, 21, 21, 33, 33, 1, 1] 201 rigid atoms, others: [45, 36, 37, 38, 39, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 247 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114065 none O=C(CCC1=CN=CC(F)=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 57, 60, 114, 114, 114, 114, 114, 114, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 57, 57, 60, 60, 114, 114, 114, 17, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [40, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 359 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114065 none O=C(CCC1=CN=CC(F)=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 38, 38, 38, 114, 114, 114, 156, 201, 201, 201, 201, 201, 114, 114, 38, 7, 7, 2, 2, 1, 1, 1, 20, 38, 38, 38, 38, 114, 156, 156, 201, 201, 38, 38] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 723 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114065 none O=C(CCC1=CN=CC(F)=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 104, 107, 201, 201, 201, 201, 201, 201, 33, 33, 33, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 33, 104, 104, 107, 107, 201, 201, 201, 49, 33, 33, 33, 33, 7, 4, 4, 2, 2, 33, 33] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 591 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114065 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114065/1 /scratch/stefan/7770410/working/building/REAL300020114065 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1748) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1748 `/scratch/stefan/7770410/working/3D/1748' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CN=CC(F)=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114065.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114065/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114065 none O=C(CCC1=CN=CC(F)=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 18, 20, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 8, 8, 8, 20, 32, 32, 32, 32, 32, 8, 8, 1, 18, 18, 20, 20, 38, 38, 38, 5, 1, 1, 1, 1, 8, 20, 20, 32, 32, 1, 1] 201 rigid atoms, others: [45, 36, 37, 38, 39, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 241 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114065 none O=C(CCC1=CN=CC(F)=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 57, 60, 113, 113, 113, 113, 113, 113, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 57, 57, 60, 60, 113, 113, 113, 17, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [40, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 354 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114065 none O=C(CCC1=CN=CC(F)=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 38, 38, 38, 113, 113, 113, 155, 201, 201, 201, 201, 201, 113, 113, 38, 7, 7, 2, 2, 1, 1, 1, 20, 38, 38, 38, 38, 113, 155, 155, 201, 201, 38, 38] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 728 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114065 none O=C(CCC1=CN=CC(F)=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 104, 107, 201, 201, 201, 201, 201, 201, 32, 32, 32, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 32, 104, 104, 107, 107, 201, 201, 201, 49, 32, 32, 32, 32, 7, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 593 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114065 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114065 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114065/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114065/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114065 Building REAL300020114066 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114066' /scratch/stefan/7770410/working/building/REAL300020114066 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114066 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114066/0 /scratch/stefan/7770410/working/building/REAL300020114066 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1749) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1749 `/scratch/stefan/7770410/working/3D/1749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=N1) `REAL300020114066.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114066 none CN1C=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 46, 49, 49, 49, 49, 11, 11, 1, 32, 32, 32, 32, 32, 32, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 31, 31, 46, 46, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 45, 46, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 290 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114066 none CN1C=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 86, 86, 38, 38, 38, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 103, 103, 103, 103, 103, 103, 86, 86, 86, 86, 38, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 371 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114066 none CN1C=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 8, 13, 13, 13, 32, 32, 32, 103, 103, 103, 168, 201, 201, 201, 201, 201, 103, 103, 32, 1, 1, 2, 2, 2, 1, 5, 5, 8, 8, 13, 32, 32, 32, 32, 103, 168, 168, 201, 201, 32, 32] 201 rigid atoms, others: [0, 1, 2, 3, 4, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 747 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114066 none CN1C=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 111, 111, 111, 49, 49, 49, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 49, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 111, 49, 49, 49, 49, 10, 6, 6, 4, 4, 49, 49] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 713 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114066 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114066/1 /scratch/stefan/7770410/working/building/REAL300020114066 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1750) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1750 `/scratch/stefan/7770410/working/3D/1750' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=N1) `REAL300020114066.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114066/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114066 none CN1C=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 48, 52, 52, 52, 52, 11, 11, 1, 31, 31, 31, 31, 31, 31, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 33, 33, 48, 48, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 45, 46, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 299 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114066 none CN1C=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 85, 85, 38, 38, 38, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 101, 101, 101, 101, 101, 101, 85, 85, 85, 85, 38, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 370 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114066 none CN1C=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 8, 13, 13, 13, 31, 31, 31, 101, 101, 101, 167, 201, 201, 201, 201, 201, 101, 101, 31, 1, 1, 2, 2, 2, 1, 5, 5, 8, 8, 13, 31, 31, 31, 31, 101, 167, 167, 201, 201, 31, 31] 201 rigid atoms, others: [0, 1, 2, 3, 4, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 751 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114066 none CN1C=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 112, 112, 112, 49, 49, 49, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 49, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 112, 49, 49, 49, 49, 10, 6, 6, 4, 4, 49, 49] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 716 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114066 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114066 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114066/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114066/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114066 Building REAL300020114067 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114067' /scratch/stefan/7770410/working/building/REAL300020114067 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114067 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114067/0 /scratch/stefan/7770410/working/building/REAL300020114067 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1751) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1751 `/scratch/stefan/7770410/working/3D/1751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1) `REAL300020114067.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114067 none COCC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 53, 19, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 29, 37, 50, 50, 50, 50, 7, 7, 1, 19, 75, 75, 75, 53, 53, 19, 6, 1, 1, 1, 1, 7, 29, 29, 37, 37, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 381 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114067 none COCC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 97, 39, 39, 39, 39, 22, 22, 22, 7, 7, 7, 1, 1, 1, 1, 1, 8, 10, 14, 14, 14, 14, 1, 1, 7, 39, 125, 125, 125, 97, 97, 39, 22, 7, 7, 7, 7, 1, 8, 8, 10, 10, 7, 7] 201 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 429 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114067 none COCC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 19, 39, 39, 39, 86, 105, 126, 126, 126, 126, 39, 39, 19, 1, 23, 23, 23, 8, 8, 1, 5, 19, 19, 19, 19, 39, 86, 86, 105, 105, 19, 19] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 26] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 472 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114067 none COCC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 133, 133, 133, 133, 111, 111, 111, 56, 56, 56, 21, 21, 21, 7, 4, 1, 1, 1, 1, 1, 1, 21, 21, 56, 133, 201, 201, 201, 201, 201, 133, 111, 56, 56, 56, 56, 21, 7, 7, 4, 4, 56, 56] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 709 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114067 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114067/1 /scratch/stefan/7770410/working/building/REAL300020114067 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1752) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1752 `/scratch/stefan/7770410/working/3D/1752' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1) `REAL300020114067.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114067 none COCC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 53, 19, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 29, 37, 50, 50, 50, 50, 7, 7, 1, 19, 75, 75, 75, 53, 53, 19, 6, 1, 1, 1, 1, 7, 29, 29, 37, 37, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 381 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114067 none COCC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 97, 39, 39, 39, 39, 22, 22, 22, 7, 7, 7, 1, 1, 1, 1, 1, 8, 10, 14, 14, 14, 14, 1, 1, 7, 39, 124, 124, 124, 97, 97, 39, 22, 7, 7, 7, 7, 1, 8, 8, 10, 10, 7, 7] 201 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 428 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114067 none COCC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 19, 39, 39, 39, 87, 106, 127, 127, 127, 127, 39, 39, 19, 1, 23, 23, 23, 8, 8, 1, 5, 19, 19, 19, 19, 39, 87, 87, 106, 106, 19, 19] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 26] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 475 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114067 none COCC1=NC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 133, 133, 133, 133, 111, 111, 111, 56, 56, 56, 22, 22, 22, 7, 4, 1, 1, 1, 1, 1, 1, 22, 22, 56, 133, 201, 201, 201, 201, 201, 133, 111, 56, 56, 56, 56, 22, 7, 7, 4, 4, 56, 56] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 708 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114067 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114067 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114067/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114067/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114067 Building REAL300020114068 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114068' /scratch/stefan/7770410/working/building/REAL300020114068 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114068 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114068/0 /scratch/stefan/7770410/working/building/REAL300020114068 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1753) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1753 `/scratch/stefan/7770410/working/3D/1753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1) `REAL300020114068.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114068 none CC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 35, 29, 23, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 21, 32, 32, 32, 32, 32, 8, 8, 1, 35, 35, 35, 35, 35, 35, 29, 29, 23, 23, 5, 1, 1, 1, 1, 8, 21, 21, 32, 32, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 256 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114068 none CC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 128, 128, 108, 81, 22, 22, 22, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 128, 128, 128, 128, 128, 128, 108, 108, 81, 81, 22, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 505 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114068 none CC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 4, 16, 16, 16, 35, 35, 35, 128, 128, 128, 176, 201, 201, 201, 201, 201, 128, 128, 35, 1, 2, 2, 2, 1, 1, 2, 2, 4, 4, 16, 35, 35, 35, 35, 128, 176, 176, 201, 201, 35, 35] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 656 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114068 none CC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 181, 151, 51, 51, 51, 32, 32, 32, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 32, 201, 201, 201, 201, 201, 201, 181, 181, 151, 151, 51, 32, 32, 32, 32, 8, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 773 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114068 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114068/1 /scratch/stefan/7770410/working/building/REAL300020114068 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1754) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1754 `/scratch/stefan/7770410/working/3D/1754' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1) `REAL300020114068.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114068 none CC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 35, 29, 23, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 20, 31, 31, 31, 31, 31, 8, 8, 1, 35, 35, 35, 35, 35, 35, 29, 29, 23, 23, 5, 1, 1, 1, 1, 8, 20, 20, 31, 31, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 253 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114068 none CC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 128, 128, 108, 81, 22, 22, 22, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 128, 128, 128, 128, 128, 128, 108, 108, 81, 81, 22, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 505 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114068 none CC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 4, 16, 16, 16, 35, 35, 35, 128, 128, 128, 175, 201, 201, 201, 201, 201, 128, 128, 35, 1, 2, 2, 2, 1, 1, 2, 2, 4, 4, 16, 35, 35, 35, 35, 128, 175, 175, 201, 201, 35, 35] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 659 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114068 none CC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 181, 151, 51, 51, 51, 32, 32, 32, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 32, 201, 201, 201, 201, 201, 201, 181, 181, 151, 151, 51, 32, 32, 32, 32, 8, 4, 4, 2, 2, 32, 32] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 773 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114068 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114068 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114068/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114068/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114068 Building REAL300020114069 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114069' /scratch/stefan/7770410/working/building/REAL300020114069 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114069 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114069/0 /scratch/stefan/7770410/working/building/REAL300020114069 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1755) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1755 `/scratch/stefan/7770410/working/3D/1755' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(C(N)=O)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114069.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114069 none CC(C)CC(C(N)=O)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 93, 36, 93, 107, 107, 36, 36, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 95, 95, 95, 95, 95, 95, 95, 95, 95, 93, 107, 107, 36, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [44, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 434 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114069 none CC(C)CC(C(N)=O)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 199, 199, 199, 89, 199, 201, 201, 89, 89, 43, 43, 43, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 43, 199, 199, 199, 199, 199, 199, 199, 199, 199, 199, 201, 201, 89, 43, 43, 43, 43, 10, 6, 6, 4, 4, 43, 43] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 788 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114069 none CC(C)CC(C(N)=O)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 24, 6, 24, 28, 28, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 48, 54, 54, 54, 54, 11, 11, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 24, 28, 28, 6, 1, 1, 1, 1, 11, 33, 33, 48, 48, 1, 1] 201 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 49, 50, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 313 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114069 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114069/1 /scratch/stefan/7770410/working/building/REAL300020114069 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1756) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1756 `/scratch/stefan/7770410/working/3D/1756' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(C(N)=O)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114069.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114069 none CC(C)CC(C(N)=O)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 92, 36, 92, 105, 105, 36, 36, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 94, 94, 94, 94, 94, 94, 94, 94, 94, 92, 105, 105, 36, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [44, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 424 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114069 none CC(C)CC(C(N)=O)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 199, 199, 199, 89, 199, 201, 201, 89, 89, 43, 43, 43, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 43, 199, 199, 199, 199, 199, 199, 199, 199, 199, 199, 201, 201, 89, 43, 43, 43, 43, 10, 6, 6, 4, 4, 43, 43] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 788 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114069 none CC(C)CC(C(N)=O)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 24, 6, 24, 28, 28, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 48, 55, 55, 55, 55, 11, 11, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 24, 28, 28, 6, 1, 1, 1, 1, 11, 33, 33, 48, 48, 1, 1] 201 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 49, 50, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 315 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114069 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114069 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114069/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114069/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114069 Building REAL300020114070 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114070' /scratch/stefan/7770410/working/building/REAL300020114070 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114070 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114070/0 /scratch/stefan/7770410/working/building/REAL300020114070 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1757) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1757 `/scratch/stefan/7770410/working/3D/1757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC(F)(F)C(F)(F)F)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114070.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114070 none O=C(CC(F)(F)C(F)(F)F)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 15, 5, 15, 15, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 78, 114, 114, 100, 114, 114, 114, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 78, 78, 30, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [34, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 578 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114070 none O=C(CC(F)(F)C(F)(F)F)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 15, 5, 15, 15, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 142, 201, 201, 187, 201, 201, 201, 38, 38, 38, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 38, 142, 142, 75, 38, 38, 38, 38, 8, 4, 4, 2, 2, 38, 38] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 937 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114070 none O=C(CC(F)(F)C(F)(F)F)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 15, 5, 15, 15, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 20, 31, 31, 27, 31, 31, 31, 1, 1, 1, 1, 1, 8, 8, 8, 24, 37, 37, 37, 37, 37, 8, 8, 1, 20, 20, 6, 1, 1, 1, 1, 8, 24, 24, 37, 37, 1, 1] 201 rigid atoms, others: [32, 33, 39, 40, 10, 11, 12, 13, 14, 26, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 34, 35, 36, 37, 38]) total number of confs: 298 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114070 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114070/1 /scratch/stefan/7770410/working/building/REAL300020114070 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1758) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1758 `/scratch/stefan/7770410/working/3D/1758' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC(F)(F)C(F)(F)F)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114070.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114070 none O=C(CC(F)(F)C(F)(F)F)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 15, 5, 15, 15, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 79, 114, 114, 100, 114, 114, 114, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 79, 79, 30, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [34, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 575 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114070 none O=C(CC(F)(F)C(F)(F)F)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 15, 5, 15, 15, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 142, 201, 201, 187, 201, 201, 201, 37, 37, 37, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 37, 142, 142, 74, 37, 37, 37, 37, 7, 4, 4, 2, 2, 37, 37] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 941 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114070 none O=C(CC(F)(F)C(F)(F)F)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 15, 5, 15, 15, 15, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 20, 31, 31, 27, 31, 31, 31, 1, 1, 1, 1, 1, 8, 8, 8, 23, 36, 36, 36, 36, 36, 8, 8, 1, 20, 20, 6, 1, 1, 1, 1, 8, 23, 23, 36, 36, 1, 1] 201 rigid atoms, others: [32, 33, 39, 40, 10, 11, 12, 13, 14, 26, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 34, 35, 36, 37, 38]) total number of confs: 295 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114070 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114070 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114070/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114070/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114070 Building REAL300020114071 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114071' /scratch/stefan/7770410/working/building/REAL300020114071 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114071 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114071/0 /scratch/stefan/7770410/working/building/REAL300020114071 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1759) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1759 `/scratch/stefan/7770410/working/3D/1759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CCC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1) `REAL300020114071.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114071 none COC1CCC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 39, 39, 39, 39, 20, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 19, 30, 30, 30, 30, 30, 7, 7, 1, 39, 39, 51, 51, 51, 39, 39, 39, 39, 39, 39, 20, 20, 5, 1, 1, 1, 1, 7, 19, 19, 30, 30, 1, 1, 39, 39, 39, 39] 201 rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 49, 50, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 51, 52, 53, 54]) total number of confs: 285 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114071 none COC1CCC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [145, 130, 130, 130, 130, 86, 15, 15, 15, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 130, 130, 145, 145, 145, 130, 130, 130, 130, 130, 130, 86, 86, 15, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 130, 130, 130, 130] 201 rigid atoms, others: [12, 44, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 525 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114071 none COC1CCC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 21, 21, 21, 39, 39, 39, 130, 130, 130, 173, 201, 201, 201, 201, 201, 130, 130, 39, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 21, 39, 39, 39, 39, 130, 173, 173, 201, 201, 39, 39, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 34, 35, 52, 53, 54, 36, 26, 27, 51, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 640 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114071 none COC1CCC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 162, 45, 45, 45, 32, 32, 32, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 32, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 162, 162, 45, 32, 32, 32, 32, 8, 4, 4, 2, 2, 32, 32, 201, 201, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 745 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114071 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114071/1 /scratch/stefan/7770410/working/building/REAL300020114071 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1760) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1760 `/scratch/stefan/7770410/working/3D/1760' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CCC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1) `REAL300020114071.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114071 none COC1CCC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 39, 39, 39, 39, 21, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 20, 31, 31, 31, 31, 31, 7, 7, 1, 39, 39, 51, 51, 51, 39, 39, 39, 39, 39, 39, 21, 21, 5, 1, 1, 1, 1, 7, 20, 20, 31, 31, 1, 1, 39, 39, 39, 39] 201 rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 49, 50, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 51, 52, 53, 54]) total number of confs: 287 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114071 none COC1CCC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [145, 130, 130, 130, 130, 86, 15, 15, 15, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 130, 130, 145, 145, 145, 130, 130, 130, 130, 130, 130, 86, 86, 15, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 130, 130, 130, 130] 201 rigid atoms, others: [12, 44, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 525 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114071 none COC1CCC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 21, 21, 21, 39, 39, 39, 130, 130, 130, 173, 201, 201, 201, 201, 201, 130, 130, 39, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 21, 39, 39, 39, 39, 130, 173, 173, 201, 201, 39, 39, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 34, 35, 52, 53, 54, 36, 26, 27, 51, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 641 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114071 none COC1CCC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 162, 43, 43, 43, 31, 31, 31, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 31, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 162, 162, 43, 31, 31, 31, 31, 7, 4, 4, 2, 2, 31, 31, 201, 201, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 746 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114071 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114071 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114071/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114071/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114071 Building REAL300020114072 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114072' /scratch/stefan/7770410/working/building/REAL300020114072 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114072 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114072/0 /scratch/stefan/7770410/working/building/REAL300020114072 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1761) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1761 `/scratch/stefan/7770410/working/3D/1761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)C(C)(C)C1(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114072.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114072 none CC1(C)C(C)(C)C1(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 11, 11, 6, 11, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 41, 59, 77, 77, 77, 77, 11, 11, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 11, 41, 41, 59, 59, 1, 1] 201 rigid atoms, others: [11, 44, 10, 43, 12, 13, 14, 45, 52, 46, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 308 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114072 none CC1(C)C(C)(C)C1(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 83, 83, 83, 48, 83, 48, 48, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 13, 13, 13, 13, 1, 1, 11, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 48, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11] 201 rigid atoms, others: [13, 14, 47, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 298 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114072 none CC1(C)C(C)(C)C1(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 83, 83, 83, 158, 201, 201, 201, 201, 201, 83, 83, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 11, 11, 11, 11, 83, 158, 158, 201, 201, 11, 11] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 784 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114072 none CC1(C)C(C)(C)C1(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 147, 201, 147, 147, 77, 77, 77, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 77, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 147, 77, 77, 77, 77, 14, 6, 6, 4, 4, 77, 77] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 623 number of broken/clashed sets: 201 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114072 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114072/1 /scratch/stefan/7770410/working/building/REAL300020114072 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1762) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1762 `/scratch/stefan/7770410/working/3D/1762' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)C(C)(C)C1(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114072.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114072/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114072 none CC1(C)C(C)(C)C1(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 11, 11, 6, 11, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 41, 59, 77, 77, 77, 77, 11, 11, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 11, 41, 41, 59, 59, 1, 1] 201 rigid atoms, others: [11, 44, 10, 43, 12, 13, 14, 45, 52, 46, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 308 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114072 none CC1(C)C(C)(C)C1(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 83, 83, 83, 48, 83, 48, 48, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 13, 13, 13, 13, 1, 1, 11, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 48, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11] 201 rigid atoms, others: [13, 14, 47, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 298 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114072 none CC1(C)C(C)(C)C1(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 83, 83, 83, 158, 201, 201, 201, 201, 201, 83, 83, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 11, 11, 11, 11, 83, 158, 158, 201, 201, 11, 11] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 784 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114072 none CC1(C)C(C)(C)C1(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 147, 201, 147, 147, 77, 77, 77, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 77, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 147, 77, 77, 77, 77, 14, 6, 6, 4, 4, 77, 77] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 623 number of broken/clashed sets: 201 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114072 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114072 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114072/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114072/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114072 Building REAL300020114073 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114073' /scratch/stefan/7770410/working/building/REAL300020114073 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114073 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114073/0 /scratch/stefan/7770410/working/building/REAL300020114073 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1763) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1763 `/scratch/stefan/7770410/working/3D/1763' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCC1) `REAL300020114073.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114073 none C=CCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 29, 16, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 31, 45, 45, 45, 45, 45, 13, 13, 1, 16, 16, 16, 16, 38, 38, 38, 29, 29, 6, 1, 1, 1, 1, 13, 31, 31, 45, 45, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 316 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114073 none C=CCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [146, 116, 98, 58, 58, 58, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 13, 98, 98, 98, 98, 146, 146, 146, 116, 116, 58, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 98, 98, 98, 98, 98, 98, 98, 98] 201 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 511 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114073 none C=CCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 4, 4, 4, 16, 16, 16, 98, 98, 98, 143, 183, 183, 183, 183, 183, 98, 98, 16, 1, 1, 1, 1, 10, 10, 10, 5, 5, 4, 16, 16, 16, 16, 98, 143, 143, 183, 183, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 44, 45, 46, 47, 48, 49, 50, 51, 23, 24, 25, 26] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 631 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114073 none C=CCC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 171, 130, 130, 130, 45, 45, 45, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 45, 171, 171, 171, 171, 201, 201, 201, 201, 201, 130, 45, 45, 45, 45, 9, 5, 5, 3, 3, 45, 45, 171, 171, 171, 171, 171, 171, 171, 171] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 673 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114073 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114073/1 /scratch/stefan/7770410/working/building/REAL300020114073 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1764) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1764 `/scratch/stefan/7770410/working/3D/1764' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCC1) `REAL300020114073.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114073/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114073 none C=CCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 29, 16, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 32, 46, 46, 46, 46, 46, 13, 13, 1, 16, 16, 16, 16, 38, 38, 38, 29, 29, 6, 1, 1, 1, 1, 13, 32, 32, 46, 46, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 322 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114073 none C=CCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [145, 116, 98, 58, 58, 58, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 13, 98, 98, 98, 98, 145, 145, 145, 116, 116, 58, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 98, 98, 98, 98, 98, 98, 98, 98] 201 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 509 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114073 none C=CCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 4, 4, 4, 16, 16, 16, 98, 98, 98, 144, 183, 183, 183, 183, 183, 98, 98, 16, 1, 1, 1, 1, 10, 10, 10, 5, 5, 4, 16, 16, 16, 16, 98, 144, 144, 183, 183, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 44, 45, 46, 47, 48, 49, 50, 51, 23, 24, 25, 26] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 631 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114073 none C=CCC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 171, 131, 131, 131, 46, 46, 46, 11, 11, 11, 5, 3, 1, 1, 1, 1, 1, 1, 11, 11, 46, 171, 171, 171, 171, 201, 201, 201, 201, 201, 131, 46, 46, 46, 46, 11, 5, 5, 3, 3, 46, 46, 171, 171, 171, 171, 171, 171, 171, 171] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 672 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114073 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114073 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114073/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114073/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114073 Building REAL300020114074 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114074' /scratch/stefan/7770410/working/building/REAL300020114074 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114074 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114074/0 /scratch/stefan/7770410/working/building/REAL300020114074 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1765) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1765 `/scratch/stefan/7770410/working/3D/1765' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCCCC1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114074.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114074 none CC1(C)CCCCC1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 53, 53, 39, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 26, 35, 45, 45, 45, 45, 7, 7, 1, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 39, 39, 6, 1, 1, 1, 1, 7, 26, 26, 35, 35, 1, 1] 201 rigid atoms, others: [15, 11, 12, 13, 14, 47, 48, 49, 46, 55, 56, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53, 54]) total number of confs: 334 number of broken/clashed sets: 92 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114074 none CC1(C)CCCCC1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 107, 107, 107, 87, 24, 24, 24, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 7, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 87, 87, 24, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7] 201 rigid atoms, others: [18, 14, 15, 16, 17, 50, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56]) total number of confs: 428 number of broken/clashed sets: 92 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114074 none CC1(C)CCCCC1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 15, 15, 15, 53, 53, 53, 107, 107, 107, 177, 201, 201, 201, 201, 201, 107, 107, 53, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 53, 53, 53, 53, 107, 177, 177, 201, 201, 53, 53] 201 rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 40, 41, 42, 36, 34, 8, 35, 4, 38, 5, 37, 39, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 731 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114074 none CC1(C)CCCCC1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 200, 95, 95, 95, 47, 47, 47, 18, 18, 18, 7, 4, 1, 1, 1, 1, 1, 1, 18, 18, 47, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 200, 200, 95, 47, 47, 47, 47, 18, 7, 7, 4, 4, 47, 47] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 727 number of broken/clashed sets: 92 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114074 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114074/1 /scratch/stefan/7770410/working/building/REAL300020114074 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1766) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1766 `/scratch/stefan/7770410/working/3D/1766' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCCCC1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114074.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114074 none CC1(C)CCCCC1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 53, 53, 39, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 26, 35, 45, 45, 45, 45, 7, 7, 1, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 39, 39, 6, 1, 1, 1, 1, 7, 26, 26, 35, 35, 1, 1] 201 rigid atoms, others: [15, 11, 12, 13, 14, 47, 48, 49, 46, 55, 56, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53, 54]) total number of confs: 334 number of broken/clashed sets: 92 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114074 none CC1(C)CCCCC1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 107, 107, 107, 87, 24, 24, 24, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 7, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 87, 87, 24, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7] 201 rigid atoms, others: [18, 14, 15, 16, 17, 50, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56]) total number of confs: 428 number of broken/clashed sets: 92 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114074 none CC1(C)CCCCC1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 15, 15, 15, 53, 53, 53, 107, 107, 107, 177, 201, 201, 201, 201, 201, 107, 107, 53, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 53, 53, 53, 53, 107, 177, 177, 201, 201, 53, 53] 201 rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 40, 41, 42, 36, 34, 8, 35, 4, 38, 5, 37, 39, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 731 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114074 none CC1(C)CCCCC1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 200, 95, 95, 95, 47, 47, 47, 18, 18, 18, 7, 4, 1, 1, 1, 1, 1, 1, 18, 18, 47, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 200, 200, 95, 47, 47, 47, 47, 18, 7, 7, 4, 4, 47, 47] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 727 number of broken/clashed sets: 92 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114074 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114074 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114074/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114074/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114074 Building REAL300020114075 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114075' /scratch/stefan/7770410/working/building/REAL300020114075 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114075 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114075/0 /scratch/stefan/7770410/working/building/REAL300020114075 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1767) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1767 `/scratch/stefan/7770410/working/3D/1767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)NC=N1) `REAL300020114075.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114075 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 3, 3, 1, 7, 7, 7, 7, 7, 7, 4, 1, 1, 1, 1, 3, 5, 5, 5, 5, 1, 1, 7, 7] 8 rigid atoms, others: [32, 5, 6, 7, 8, 9, 39, 21, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 29 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114075 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 4, 4, 4, 3, 3, 3, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 3, 7, 7, 7, 7, 7, 7, 4, 3, 3, 3, 3, 1, 5, 5, 5, 5, 3, 3, 7, 7] 8 rigid atoms, others: [33, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 31 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114075 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 7, 7, 7, 1, 1, 1, 2, 2, 2, 4, 7, 7, 7, 7, 7, 8, 8, 8, 8, 7, 7, 1, 1] 8 rigid atoms, others: [0, 1, 2, 3, 40, 41, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114075 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 6, 6, 6, 5, 5, 5, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 8, 6, 5, 5, 5, 5, 5, 3, 3, 1, 1, 5, 5, 8, 8] 8 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 21 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114075 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114075/1 /scratch/stefan/7770410/working/building/REAL300020114075 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1768) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1768 `/scratch/stefan/7770410/working/3D/1768' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)NC=N1) `REAL300020114075.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114075/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114075 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 3, 3, 1, 7, 7, 7, 7, 7, 7, 4, 1, 1, 1, 1, 3, 5, 5, 5, 5, 1, 1, 7, 7] 8 rigid atoms, others: [32, 5, 6, 7, 8, 9, 39, 21, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 29 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114075 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 4, 4, 4, 3, 3, 3, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 3, 7, 7, 7, 7, 7, 7, 4, 3, 3, 3, 3, 1, 5, 5, 5, 5, 3, 3, 7, 7] 8 rigid atoms, others: [33, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 31 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114075 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 7, 7, 7, 1, 1, 1, 2, 2, 2, 4, 7, 7, 7, 7, 7, 8, 8, 8, 8, 7, 7, 1, 1] 8 rigid atoms, others: [0, 1, 2, 3, 40, 41, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114075 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 6, 6, 6, 5, 5, 5, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 8, 6, 5, 5, 5, 5, 5, 3, 3, 1, 1, 5, 5, 8, 8] 8 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 21 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114075 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114075 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114075/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114075/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114075 Building REAL300020114076 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114076' /scratch/stefan/7770410/working/building/REAL300020114076 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114076 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114076/0 /scratch/stefan/7770410/working/building/REAL300020114076 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1769) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1769 `/scratch/stefan/7770410/working/3D/1769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)N1CCOCC1) `REAL300020114076.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114076 none C[C@@H](C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 42, 92, 42, 42, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 92, 108, 108, 108, 108, 108, 92, 92, 92, 42, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 108, 108, 108, 108, 108, 108, 108, 108] 201 rigid atoms, others: [36, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 390 number of broken/clashed sets: 98 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114076 none C[C@@H](C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 135, 200, 135, 135, 59, 59, 59, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 59, 200, 201, 201, 201, 201, 201, 200, 200, 200, 135, 59, 59, 59, 59, 11, 6, 6, 4, 4, 59, 59, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 695 number of broken/clashed sets: 93 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114076 none C[C@@H](C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 6, 21, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 36, 51, 62, 62, 62, 62, 11, 11, 1, 21, 29, 29, 29, 29, 29, 21, 21, 21, 6, 1, 1, 1, 1, 11, 36, 36, 51, 51, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 42, 21, 41] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 311 number of broken/clashed sets: 98 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114076 none C[C@@H](C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 12, 12, 12, 29, 29, 29, 108, 108, 108, 166, 201, 201, 201, 201, 201, 108, 108, 29, 1, 1, 1, 1, 1, 1, 7, 7, 7, 12, 29, 29, 29, 29, 108, 166, 166, 201, 201, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 43, 44, 45, 46, 47, 48, 49, 50, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 696 number of broken/clashed sets: 98 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114076 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114076/1 /scratch/stefan/7770410/working/building/REAL300020114076 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1770) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1770 `/scratch/stefan/7770410/working/3D/1770' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)N1CCOCC1) `REAL300020114076.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114076 none C[C@@H](C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 40, 91, 40, 40, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 91, 110, 110, 110, 110, 110, 91, 91, 91, 40, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 110, 110, 110, 110, 110, 110, 110, 110] 201 rigid atoms, others: [36, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 395 number of broken/clashed sets: 94 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114076 none C[C@@H](C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 135, 200, 135, 135, 58, 58, 58, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 58, 200, 201, 201, 201, 201, 201, 200, 200, 200, 135, 58, 58, 58, 58, 10, 6, 6, 4, 4, 58, 58, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 695 number of broken/clashed sets: 93 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114076 none C[C@@H](C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 6, 21, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 35, 50, 61, 61, 61, 61, 11, 11, 1, 21, 29, 29, 29, 29, 29, 21, 21, 21, 6, 1, 1, 1, 1, 11, 35, 35, 50, 50, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 42, 21, 41] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 305 number of broken/clashed sets: 94 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114076 none C[C@@H](C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 12, 12, 12, 29, 29, 29, 110, 110, 110, 166, 201, 201, 201, 201, 201, 110, 110, 29, 1, 1, 1, 1, 1, 1, 7, 7, 7, 12, 29, 29, 29, 29, 110, 166, 166, 201, 201, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 43, 44, 45, 46, 47, 48, 49, 50, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 690 number of broken/clashed sets: 94 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114076 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114076 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114076/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114076/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114076 Building REAL300020114077 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114077' /scratch/stefan/7770410/working/building/REAL300020114077 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114077 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114077/0 /scratch/stefan/7770410/working/building/REAL300020114077 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1771) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1771 `/scratch/stefan/7770410/working/3D/1771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1) `REAL300020114077.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114077 none CC(C)OC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 17, 31, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 35, 45, 46, 46, 46, 46, 10, 10, 1, 6, 6, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 1, 1, 1, 1, 10, 35, 35, 45, 45, 1, 1, 6] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50]) total number of confs: 280 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114077 none CC(C)OC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [141, 109, 141, 37, 37, 37, 37, 37, 37, 37, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 10, 37, 37, 141, 141, 141, 141, 141, 141, 141, 37, 37, 37, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 37] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 419 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114077 none CC(C)OC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 37, 37, 37, 101, 121, 122, 122, 122, 122, 37, 37, 6, 1, 1, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 6, 6, 6, 6, 37, 101, 101, 121, 121, 6, 6, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 38, 50, 36, 27, 28, 37] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 488 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114077 none CC(C)OC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 122, 122, 122, 122, 122, 122, 122, 46, 46, 46, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 46, 122, 122, 201, 201, 201, 201, 201, 201, 201, 122, 122, 122, 46, 46, 46, 46, 9, 5, 5, 3, 3, 46, 46, 122] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 467 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114077 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114077/1 /scratch/stefan/7770410/working/building/REAL300020114077 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1772) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1772 `/scratch/stefan/7770410/working/3D/1772' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1) `REAL300020114077.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114077/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114077 none CC(C)OC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 17, 31, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 35, 45, 46, 46, 46, 46, 10, 10, 1, 6, 6, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 1, 1, 1, 1, 10, 35, 35, 45, 45, 1, 1, 6] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50]) total number of confs: 280 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114077 none CC(C)OC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [141, 109, 141, 37, 37, 37, 37, 37, 37, 37, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 10, 37, 37, 141, 141, 141, 141, 141, 141, 141, 37, 37, 37, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 37] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 419 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114077 none CC(C)OC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 37, 37, 37, 101, 121, 122, 122, 122, 122, 37, 37, 6, 1, 1, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 6, 6, 6, 6, 37, 101, 101, 121, 121, 6, 6, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 38, 50, 36, 27, 28, 37] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 488 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114077 none CC(C)OC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 122, 122, 122, 122, 122, 122, 122, 45, 45, 45, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 45, 122, 122, 201, 201, 201, 201, 201, 201, 201, 122, 122, 122, 45, 45, 45, 45, 8, 4, 4, 2, 2, 45, 45, 122] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 466 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114077 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114077 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114077/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114077/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114077 Building REAL300020114078 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114078' /scratch/stefan/7770410/working/building/REAL300020114078 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114078 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114078/0 /scratch/stefan/7770410/working/building/REAL300020114078 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1773) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1773 `/scratch/stefan/7770410/working/3D/1773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC12CCOCC2) `REAL300020114078.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114078 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC12CCOCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 13, 58, 127, 127, 127, 127, 127, 127, 127, 58, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 398 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114078 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC12CCOCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 46, 46, 46, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 46, 131, 201, 201, 201, 201, 201, 201, 201, 131, 46, 46, 46, 46, 7, 4, 4, 2, 2, 46, 46, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 600 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114078 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC12CCOCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 31, 45, 45, 45, 45, 45, 13, 13, 1, 6, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 13, 31, 31, 45, 45, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114078 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC12CCOCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 20, 20, 20, 127, 127, 127, 170, 201, 201, 201, 201, 201, 127, 127, 20, 1, 1, 1, 1, 1, 1, 1, 1, 5, 20, 20, 20, 20, 127, 170, 170, 201, 201, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 588 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114078 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114078/1 /scratch/stefan/7770410/working/building/REAL300020114078 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1774) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1774 `/scratch/stefan/7770410/working/3D/1774' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC12CCOCC2) `REAL300020114078.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114078/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114078 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC12CCOCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 13, 58, 127, 127, 127, 127, 127, 127, 127, 58, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 398 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114078 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC12CCOCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 45, 45, 45, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 45, 131, 201, 201, 201, 201, 201, 201, 201, 131, 45, 45, 45, 45, 7, 4, 4, 2, 2, 45, 45, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 602 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114078 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC12CCOCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 31, 45, 45, 45, 45, 45, 13, 13, 1, 6, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 13, 31, 31, 45, 45, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114078 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC12CCOCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 20, 20, 20, 127, 127, 127, 170, 201, 201, 201, 201, 201, 127, 127, 20, 1, 1, 1, 1, 1, 1, 1, 1, 5, 20, 20, 20, 20, 127, 170, 170, 201, 201, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 588 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114078 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114078 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114078/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114078/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114078 Building REAL300020114079 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114079' /scratch/stefan/7770410/working/building/REAL300020114079 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114079 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114079/0 /scratch/stefan/7770410/working/building/REAL300020114079 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1775) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1775 `/scratch/stefan/7770410/working/3D/1775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1) `REAL300020114079.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114079 none CC1(C)CCC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 35, 35, 21, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 21, 32, 32, 32, 32, 32, 7, 7, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 21, 21, 5, 1, 1, 1, 1, 7, 21, 21, 32, 32, 1, 1, 35, 35, 35, 35] 201 rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 44, 51, 52, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50, 53, 54, 55, 56]) total number of confs: 260 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114079 none CC1(C)CCC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 114, 114, 88, 15, 15, 15, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 114, 114, 114, 114, 114, 114, 114, 114, 114, 114, 114, 114, 114, 88, 88, 15, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7, 114, 114, 114, 114] 201 rigid atoms, others: [12, 13, 46, 15, 16, 14, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 438 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114079 none CC1(C)CCC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 19, 19, 19, 35, 35, 35, 114, 114, 114, 160, 201, 201, 201, 201, 201, 114, 114, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 19, 35, 35, 35, 35, 114, 160, 160, 201, 201, 35, 35, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 53, 54, 55, 56] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 697 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114079 none CC1(C)CCC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 189, 44, 44, 44, 32, 32, 32, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 32, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 189, 189, 44, 32, 32, 32, 32, 8, 4, 4, 2, 2, 32, 32, 201, 201, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 719 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114079 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114079/1 /scratch/stefan/7770410/working/building/REAL300020114079 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1776) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1776 `/scratch/stefan/7770410/working/3D/1776' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1) `REAL300020114079.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114079 none CC1(C)CCC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 34, 34, 21, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 21, 32, 32, 32, 32, 32, 7, 7, 1, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 21, 21, 5, 1, 1, 1, 1, 7, 21, 21, 32, 32, 1, 1, 34, 34, 34, 34] 201 rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 44, 51, 52, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50, 53, 54, 55, 56]) total number of confs: 256 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114079 none CC1(C)CCC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 113, 113, 87, 15, 15, 15, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 113, 113, 113, 113, 113, 113, 113, 113, 113, 113, 113, 113, 113, 87, 87, 15, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7, 113, 113, 113, 113] 201 rigid atoms, others: [12, 13, 46, 15, 16, 14, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 435 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114079 none CC1(C)CCC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 18, 18, 18, 34, 34, 34, 113, 113, 113, 159, 201, 201, 201, 201, 201, 113, 113, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 34, 34, 34, 34, 113, 159, 159, 201, 201, 34, 34, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 53, 54, 55, 56] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 701 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114079 none CC1(C)CCC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 189, 44, 44, 44, 32, 32, 32, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 32, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 189, 189, 44, 32, 32, 32, 32, 8, 4, 4, 2, 2, 32, 32, 201, 201, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 719 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114079 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114079 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114079/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114079/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114079 Building REAL300020114080 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114080' /scratch/stefan/7770410/working/building/REAL300020114080 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114080 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114080/0 /scratch/stefan/7770410/working/building/REAL300020114080 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1777) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1777 `/scratch/stefan/7770410/working/3D/1777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCOCC1) `REAL300020114080.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114080 none CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 40, 40, 40, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 91, 100, 100, 100, 100, 100, 91, 91, 91, 91, 40, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 100, 100, 100, 100, 100, 100, 100, 100, 100] 201 rigid atoms, others: [36, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 410 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114080 none CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 139, 139, 139, 60, 60, 60, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 60, 200, 201, 201, 201, 201, 201, 200, 200, 200, 200, 139, 60, 60, 60, 60, 11, 6, 6, 4, 4, 60, 60, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 716 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114080 none CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 49, 61, 61, 61, 61, 11, 11, 1, 19, 26, 26, 26, 26, 26, 19, 19, 19, 19, 6, 1, 1, 1, 1, 11, 33, 33, 49, 49, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 41, 42, 20] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 314 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114080 none CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 10, 10, 10, 26, 26, 26, 100, 100, 100, 169, 201, 201, 201, 201, 201, 100, 100, 26, 1, 1, 1, 1, 1, 1, 5, 5, 5, 4, 10, 26, 26, 26, 26, 100, 169, 169, 201, 201, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 43, 44, 45, 46, 47, 48, 49, 50, 51, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 720 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114080 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114080/1 /scratch/stefan/7770410/working/building/REAL300020114080 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1778) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1778 `/scratch/stefan/7770410/working/3D/1778' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCOCC1) `REAL300020114080.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114080 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 40, 40, 40, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 91, 100, 100, 100, 100, 100, 91, 91, 91, 91, 40, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 100, 100, 100, 100, 100, 100, 100, 100, 100] 201 rigid atoms, others: [36, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 410 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114080 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 139, 139, 139, 60, 60, 60, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 60, 200, 201, 201, 201, 201, 201, 200, 200, 200, 200, 139, 60, 60, 60, 60, 11, 6, 6, 4, 4, 60, 60, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 716 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114080 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 49, 61, 61, 61, 61, 11, 11, 1, 19, 26, 26, 26, 26, 26, 19, 19, 19, 19, 6, 1, 1, 1, 1, 11, 33, 33, 49, 49, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 41, 42, 20] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 314 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114080 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 10, 10, 10, 26, 26, 26, 100, 100, 100, 169, 201, 201, 201, 201, 201, 100, 100, 26, 1, 1, 1, 1, 1, 1, 5, 5, 5, 4, 10, 26, 26, 26, 26, 100, 169, 169, 201, 201, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 43, 44, 45, 46, 47, 48, 49, 50, 51, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 720 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114080 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114080 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114080/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114080/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114080 Building REAL300020114081 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114081' /scratch/stefan/7770410/working/building/REAL300020114081 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114081 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114081/0 /scratch/stefan/7770410/working/building/REAL300020114081 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1779) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1779 `/scratch/stefan/7770410/working/3D/1779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CC(=O)NC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114081.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114081 none O=C(CC1CC(=O)NC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 11, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 43, 75, 75, 75, 75, 75, 75, 1, 1, 1, 1, 1, 6, 6, 6, 14, 20, 20, 20, 20, 20, 6, 6, 1, 43, 43, 75, 75, 75, 75, 6, 1, 1, 1, 1, 6, 14, 14, 20, 20, 1, 1] 119 rigid atoms, others: [34, 35, 36, 37, 44, 10, 11, 12, 13, 14, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 327 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114081 none O=C(CC1CC(=O)NC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 11, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 75, 96, 96, 96, 96, 96, 96, 6, 6, 6, 1, 1, 1, 1, 1, 7, 9, 9, 9, 9, 9, 1, 1, 6, 75, 75, 96, 96, 96, 96, 19, 6, 6, 6, 6, 1, 7, 7, 9, 9, 6, 6] 119 rigid atoms, others: [38, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 374 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114081 none O=C(CC1CC(=O)NC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 11, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [36, 8, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 75, 75, 75, 96, 96, 96, 115, 119, 119, 119, 119, 119, 96, 96, 75, 8, 8, 1, 1, 1, 1, 36, 75, 75, 75, 75, 96, 115, 115, 119, 119, 75, 75] 119 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 378 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114081 none O=C(CC1CC(=O)NC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 11, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 104, 120, 120, 120, 120, 120, 120, 23, 23, 23, 12, 12, 12, 6, 2, 1, 1, 1, 1, 1, 1, 12, 12, 23, 104, 104, 120, 120, 120, 120, 41, 23, 23, 23, 23, 12, 6, 6, 2, 2, 23, 23] 120 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 451 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114081 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114081/1 /scratch/stefan/7770410/working/building/REAL300020114081 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1780) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1780 `/scratch/stefan/7770410/working/3D/1780' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CC(=O)NC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114081.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114081/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114081 none O=C(CC1CC(=O)NC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 11, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 42, 73, 73, 73, 73, 73, 73, 1, 1, 1, 1, 1, 6, 6, 6, 14, 19, 19, 19, 19, 19, 6, 6, 1, 42, 42, 73, 73, 73, 73, 6, 1, 1, 1, 1, 6, 14, 14, 19, 19, 1, 1] 116 rigid atoms, others: [34, 35, 36, 37, 44, 10, 11, 12, 13, 14, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 316 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114081 none O=C(CC1CC(=O)NC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 11, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 73, 93, 93, 93, 93, 93, 93, 6, 6, 6, 1, 1, 1, 1, 1, 7, 9, 9, 9, 9, 9, 1, 1, 6, 73, 73, 93, 93, 93, 93, 19, 6, 6, 6, 6, 1, 7, 7, 9, 9, 6, 6] 116 rigid atoms, others: [38, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 361 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114081 none O=C(CC1CC(=O)NC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 11, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [35, 8, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 73, 73, 73, 93, 93, 93, 112, 116, 116, 116, 116, 116, 93, 93, 73, 8, 8, 1, 1, 1, 1, 35, 73, 73, 73, 73, 93, 112, 112, 116, 116, 73, 73] 116 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 372 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114081 none O=C(CC1CC(=O)NC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 11, 8, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 101, 116, 116, 116, 116, 116, 116, 22, 22, 22, 12, 12, 12, 6, 2, 1, 1, 1, 1, 1, 1, 12, 12, 22, 101, 101, 116, 116, 116, 116, 40, 22, 22, 22, 22, 12, 6, 6, 2, 2, 22, 22] 116 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 439 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114081 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114081 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114081/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114081/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114081 Building REAL300020114082 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114082' /scratch/stefan/7770410/working/building/REAL300020114082 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114082 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114082/0 /scratch/stefan/7770410/working/building/REAL300020114082 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1781) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1781 `/scratch/stefan/7770410/working/3D/1781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1C(C)C) `REAL300020114082.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114082 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 54, 72, 91, 91, 91, 91, 11, 11, 1, 10, 10, 10, 23, 23, 10, 10, 10, 10, 6, 1, 1, 1, 1, 11, 54, 54, 72, 72, 1, 1, 23, 23, 23, 23, 23, 23, 23] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 398 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114082 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 46, 46, 46, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 11, 61, 61, 61, 112, 112, 61, 61, 61, 61, 46, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 112, 112, 112, 112, 112, 112, 112] 201 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 448 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114082 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 61, 61, 61, 142, 183, 201, 201, 201, 201, 61, 61, 10, 1, 1, 1, 3, 3, 2, 2, 2, 1, 4, 10, 10, 10, 10, 61, 142, 142, 183, 183, 10, 10, 3, 4, 4, 4, 3, 3, 3] 201 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 765 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114082 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 190, 190, 190, 91, 91, 91, 20, 20, 20, 6, 4, 1, 1, 1, 1, 1, 1, 20, 20, 91, 201, 201, 201, 201, 201, 201, 201, 201, 201, 190, 91, 91, 91, 91, 20, 6, 6, 4, 4, 91, 91, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 536 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114082 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114082/1 /scratch/stefan/7770410/working/building/REAL300020114082 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1782) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1782 `/scratch/stefan/7770410/working/3D/1782' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1C(C)C) `REAL300020114082.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114082 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 53, 71, 89, 89, 89, 89, 11, 11, 1, 10, 10, 10, 25, 25, 10, 10, 10, 10, 6, 1, 1, 1, 1, 11, 53, 53, 71, 71, 1, 1, 25, 25, 25, 25, 25, 25, 25] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 399 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114082 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 46, 46, 46, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 11, 62, 62, 62, 111, 111, 62, 62, 62, 62, 46, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 111, 111, 111, 111, 111, 111, 111] 201 rigid atoms, others: [37, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 447 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114082 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 62, 62, 62, 142, 183, 201, 201, 201, 201, 62, 62, 10, 1, 1, 1, 3, 3, 2, 2, 2, 1, 4, 10, 10, 10, 10, 62, 142, 142, 183, 183, 10, 10, 3, 4, 4, 4, 3, 3, 3] 201 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 763 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114082 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 190, 190, 190, 90, 90, 90, 19, 19, 19, 6, 4, 1, 1, 1, 1, 1, 1, 19, 19, 90, 201, 201, 201, 201, 201, 201, 201, 201, 201, 190, 90, 90, 90, 90, 19, 6, 6, 4, 4, 90, 90, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 539 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114082 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114082 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114082/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114082/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114082 Building REAL300020114083 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114083' /scratch/stefan/7770410/working/building/REAL300020114083 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114083 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114083/0 /scratch/stefan/7770410/working/building/REAL300020114083 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1783) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1783 `/scratch/stefan/7770410/working/3D/1783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1OC(=O)N2) `REAL300020114083.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114083 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1OC(=O)N2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 1, 11, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 11, 50, 100, 100, 100, 100, 100, 100, 100, 100, 100, 50, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 100, 100, 100, 100] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 244 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114083 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1OC(=O)N2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 1, 11, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [168, 168, 82, 82, 82, 16, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 82, 168, 201, 201, 201, 201, 201, 201, 201, 201, 201, 168, 82, 82, 82, 82, 16, 6, 6, 4, 4, 82, 82, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 517 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114083 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1OC(=O)N2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 1, 11, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 53, 71, 82, 82, 82, 82, 11, 11, 1, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 11, 53, 53, 71, 71, 1, 1, 19, 19, 19, 19] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 328 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114083 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1OC(=O)N2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 1, 11, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 19, 19, 19, 100, 100, 100, 177, 201, 201, 201, 201, 201, 100, 100, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 19, 19, 19, 19, 100, 177, 177, 201, 201, 19, 19, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 687 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114083 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114083/1 /scratch/stefan/7770410/working/building/REAL300020114083 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1784) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1784 `/scratch/stefan/7770410/working/3D/1784' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1OC(=O)N2) `REAL300020114083.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114083 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1OC(=O)N2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 1, 11, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 11, 50, 101, 101, 101, 101, 101, 101, 101, 101, 101, 50, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 101, 101, 101, 101] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 245 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114083 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1OC(=O)N2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 1, 11, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [170, 170, 84, 84, 84, 16, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 84, 170, 201, 201, 201, 201, 201, 201, 201, 201, 201, 170, 84, 84, 84, 84, 16, 6, 6, 4, 4, 84, 84, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 522 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114083 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1OC(=O)N2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 1, 11, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 54, 72, 84, 84, 84, 84, 11, 11, 1, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 11, 54, 54, 72, 72, 1, 1, 19, 19, 19, 19] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 333 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114083 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1OC(=O)N2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 12, 1, 11, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 19, 19, 19, 101, 101, 101, 176, 201, 201, 201, 201, 201, 101, 101, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 19, 19, 19, 19, 101, 176, 176, 201, 201, 19, 19, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 685 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114083 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114083 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114083/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114083/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114083 Building REAL300020114084 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114084' /scratch/stefan/7770410/working/building/REAL300020114084 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114084 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114084/0 /scratch/stefan/7770410/working/building/REAL300020114084 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1785) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1785 `/scratch/stefan/7770410/working/3D/1785' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCC(=O)N1) `REAL300020114084.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114084 none CC1(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 25, 25, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 25, 39, 41, 41, 41, 41, 8, 8, 1, 32, 32, 32, 32, 32, 32, 32, 32, 25, 25, 25, 25, 5, 1, 1, 1, 1, 8, 25, 25, 39, 39, 1, 1, 32, 32, 32, 32, 32] 201 rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 39, 45, 46, 22, 38] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51]) total number of confs: 276 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114084 none CC1(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 107, 107, 24, 24, 24, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 117, 117, 117, 117, 117, 117, 117, 117, 107, 107, 107, 107, 24, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 117, 117, 117, 117, 117] 201 rigid atoms, others: [40, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 429 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114084 none CC1(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 13, 13, 13, 32, 32, 32, 117, 117, 117, 176, 201, 201, 201, 201, 201, 117, 117, 32, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 13, 32, 32, 32, 32, 117, 176, 176, 201, 201, 32, 32, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 47, 48, 49, 50, 51, 23, 24, 25, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 685 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114084 none CC1(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 77, 77, 77, 42, 42, 42, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 42, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 77, 42, 42, 42, 42, 10, 5, 5, 3, 3, 42, 42, 201, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 749 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114084 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114084/1 /scratch/stefan/7770410/working/building/REAL300020114084 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1786) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1786 `/scratch/stefan/7770410/working/3D/1786' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC(=O)N1) `REAL300020114084.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114084 none CC1(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 25, 25, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 25, 39, 41, 41, 41, 41, 8, 8, 1, 32, 32, 32, 32, 32, 32, 32, 32, 25, 25, 25, 25, 5, 1, 1, 1, 1, 8, 25, 25, 39, 39, 1, 1, 32, 32, 32, 32, 32] 201 rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 39, 45, 46, 22, 38] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51]) total number of confs: 276 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114084 none CC1(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 106, 106, 24, 24, 24, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 117, 117, 117, 117, 117, 117, 117, 117, 106, 106, 106, 106, 24, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 117, 117, 117, 117, 117] 201 rigid atoms, others: [40, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 430 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114084 none CC1(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 13, 13, 13, 32, 32, 32, 117, 117, 117, 175, 201, 201, 201, 201, 201, 117, 117, 32, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 13, 32, 32, 32, 32, 117, 175, 175, 201, 201, 32, 32, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 47, 48, 49, 50, 51, 23, 24, 25, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 685 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114084 none CC1(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 77, 77, 77, 42, 42, 42, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 42, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 77, 42, 42, 42, 42, 10, 5, 5, 3, 3, 42, 42, 201, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 749 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114084 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114084 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114084/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114084/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114084 Building REAL300020114085 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114085' /scratch/stefan/7770410/working/building/REAL300020114085 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114085 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114085/0 /scratch/stefan/7770410/working/building/REAL300020114085 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1787) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1787 `/scratch/stefan/7770410/working/3D/1787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=CN=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114085.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114085 none CCOC1=CC=CN=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 61, 21, 21, 21, 21, 21, 21, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 33, 38, 49, 49, 49, 49, 7, 7, 1, 102, 102, 102, 102, 102, 21, 21, 21, 5, 1, 1, 1, 1, 7, 33, 33, 38, 38, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 422 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114085 none CCOC1=CC=CN=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [146, 109, 53, 53, 53, 53, 53, 53, 18, 18, 18, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 7, 146, 146, 146, 146, 146, 53, 53, 53, 18, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 419 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114085 none CCOC1=CC=CN=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 8, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 21, 21, 21, 53, 53, 53, 127, 133, 156, 156, 156, 156, 53, 53, 21, 28, 28, 28, 28, 28, 1, 1, 1, 10, 21, 21, 21, 21, 53, 127, 127, 133, 133, 21, 21] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 586 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114085 none CCOC1=CC=CN=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 164, 164, 164, 164, 164, 164, 98, 98, 98, 58, 58, 58, 22, 22, 22, 6, 4, 1, 1, 1, 1, 1, 1, 22, 22, 58, 201, 201, 201, 201, 201, 164, 164, 164, 98, 58, 58, 58, 58, 22, 6, 6, 4, 4, 58, 58] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 475 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114085 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114085/1 /scratch/stefan/7770410/working/building/REAL300020114085 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1788) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1788 `/scratch/stefan/7770410/working/3D/1788' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=CN=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114085.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114085 none CCOC1=CC=CN=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 60, 21, 21, 21, 21, 21, 21, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 33, 38, 49, 49, 49, 49, 7, 7, 1, 102, 102, 102, 102, 102, 21, 21, 21, 5, 1, 1, 1, 1, 7, 33, 33, 38, 38, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 427 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114085 none CCOC1=CC=CN=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [146, 107, 53, 53, 53, 53, 53, 53, 18, 18, 18, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 7, 146, 146, 146, 146, 146, 53, 53, 53, 18, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 429 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114085 none CCOC1=CC=CN=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 8, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 21, 21, 21, 53, 53, 53, 127, 133, 156, 156, 156, 156, 53, 53, 21, 28, 28, 28, 28, 28, 1, 1, 1, 10, 21, 21, 21, 21, 53, 127, 127, 133, 133, 21, 21] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 586 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114085 none CCOC1=CC=CN=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 165, 165, 165, 165, 165, 165, 97, 97, 97, 58, 58, 58, 22, 22, 22, 6, 4, 1, 1, 1, 1, 1, 1, 22, 22, 58, 201, 201, 201, 201, 201, 165, 165, 165, 97, 58, 58, 58, 58, 22, 6, 6, 4, 4, 58, 58] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 469 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114085 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114085 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114085/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114085/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114085 Building REAL300020114086 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114086' /scratch/stefan/7770410/working/building/REAL300020114086 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114086 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114086/0 /scratch/stefan/7770410/working/building/REAL300020114086 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1789) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1789 `/scratch/stefan/7770410/working/3D/1789' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC1=NC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114086.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114086 none CC(C)OC1=NC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 25, 36, 12, 12, 12, 12, 12, 12, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 37, 51, 57, 57, 57, 57, 9, 9, 1, 36, 36, 36, 36, 36, 36, 36, 12, 12, 12, 6, 1, 1, 1, 1, 9, 37, 37, 51, 51, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 16, 49, 50, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 323 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114086 none CC(C)OC1=NC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 84, 117, 62, 62, 62, 62, 62, 62, 29, 29, 29, 9, 9, 9, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 9, 117, 117, 117, 117, 117, 117, 117, 62, 62, 62, 29, 9, 9, 9, 9, 1, 8, 8, 10, 10, 9, 9] 201 rigid atoms, others: [44, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 408 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114086 none CC(C)OC1=NC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 10, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 62, 62, 62, 146, 189, 198, 198, 198, 198, 62, 62, 12, 10, 10, 10, 9, 10, 10, 10, 1, 1, 1, 4, 12, 12, 12, 12, 62, 146, 146, 189, 189, 12, 12] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 36, 38, 37] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 781 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114086 none CC(C)OC1=NC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 198, 198, 198, 198, 198, 198, 112, 112, 112, 57, 57, 57, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 57, 201, 201, 201, 201, 201, 201, 201, 198, 198, 198, 112, 57, 57, 57, 57, 12, 6, 6, 4, 4, 57, 57] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 465 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114086 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114086/1 /scratch/stefan/7770410/working/building/REAL300020114086 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1790) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1790 `/scratch/stefan/7770410/working/3D/1790' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC1=NC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114086.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114086/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114086 none CC(C)OC1=NC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 25, 37, 12, 12, 12, 12, 12, 12, 6, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 38, 52, 58, 58, 58, 58, 9, 9, 1, 37, 37, 37, 37, 37, 37, 37, 12, 12, 12, 6, 1, 1, 1, 1, 9, 38, 38, 52, 52, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 16, 49, 50, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 332 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114086 none CC(C)OC1=NC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 84, 118, 62, 62, 62, 62, 62, 62, 29, 29, 29, 9, 9, 9, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 9, 118, 118, 118, 118, 118, 118, 118, 62, 62, 62, 29, 9, 9, 9, 9, 1, 8, 8, 10, 10, 9, 9] 201 rigid atoms, others: [44, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 415 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114086 none CC(C)OC1=NC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 10, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 62, 62, 62, 148, 190, 198, 198, 198, 198, 62, 62, 12, 10, 10, 10, 9, 10, 10, 10, 1, 1, 1, 4, 12, 12, 12, 12, 62, 148, 148, 190, 190, 12, 12] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 36, 38, 37] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 782 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114086 none CC(C)OC1=NC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 198, 198, 198, 198, 198, 198, 113, 113, 113, 58, 58, 58, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 58, 201, 201, 201, 201, 201, 201, 201, 198, 198, 198, 113, 58, 58, 58, 58, 12, 6, 6, 4, 4, 58, 58] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 464 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114086 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114086 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114086/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114086/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114086 Building REAL300020114087 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114087' /scratch/stefan/7770410/working/building/REAL300020114087 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114087 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114087/0 /scratch/stefan/7770410/working/building/REAL300020114087 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1791) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1791 `/scratch/stefan/7770410/working/3D/1791' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN2CCCCC2=C1) `REAL300020114087.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114087 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN2CCCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 7, 7, 7, 1, 1, 1, 1, 1, 8, 12, 16, 16, 16, 16, 1, 1, 7, 16, 46, 46, 46, 46, 46, 46, 46, 46, 16, 7, 7, 7, 7, 1, 8, 8, 12, 12, 7, 7, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46] 139 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 141 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114087 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN2CCCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 55, 55, 55, 23, 23, 23, 6, 4, 1, 1, 1, 1, 1, 1, 23, 23, 55, 66, 139, 139, 139, 139, 139, 139, 139, 139, 66, 55, 55, 55, 55, 23, 6, 6, 4, 4, 55, 55, 139, 139, 139, 139, 139, 139, 139, 139, 139, 139] 139 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 291 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114087 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN2CCCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 32, 43, 51, 51, 51, 51, 7, 7, 1, 6, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 7, 32, 32, 43, 43, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 139 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114087 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN2CCCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 19, 19, 19, 46, 46, 46, 113, 139, 139, 139, 139, 139, 46, 46, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 19, 19, 19, 19, 46, 113, 113, 139, 139, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 139 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 543 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114087 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114087/1 /scratch/stefan/7770410/working/building/REAL300020114087 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1792) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1792 `/scratch/stefan/7770410/working/3D/1792' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN2CCCCC2=C1) `REAL300020114087.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114087 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN2CCCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 7, 7, 7, 1, 1, 1, 1, 1, 8, 12, 16, 16, 16, 16, 1, 1, 7, 16, 46, 46, 46, 46, 46, 46, 46, 46, 16, 7, 7, 7, 7, 1, 8, 8, 12, 12, 7, 7, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46] 140 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 141 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114087 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN2CCCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 56, 56, 56, 23, 23, 23, 6, 4, 1, 1, 1, 1, 1, 1, 23, 23, 56, 67, 140, 140, 140, 140, 140, 140, 140, 140, 67, 56, 56, 56, 56, 23, 6, 6, 4, 4, 56, 56, 140, 140, 140, 140, 140, 140, 140, 140, 140, 140] 140 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 293 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114087 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN2CCCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 32, 43, 51, 51, 51, 51, 7, 7, 1, 6, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 7, 32, 32, 43, 43, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 140 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114087 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN2CCCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 19, 19, 19, 46, 46, 46, 113, 140, 140, 140, 140, 140, 46, 46, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 19, 19, 19, 19, 46, 113, 113, 140, 140, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 140 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 549 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114087 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114087 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114087/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114087/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114087 Building REAL300020114088 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114088' /scratch/stefan/7770410/working/building/REAL300020114088 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114088 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114088/0 /scratch/stefan/7770410/working/building/REAL300020114088 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1793) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1793 `/scratch/stefan/7770410/working/3D/1793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CC=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020114088.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114088 none NC(=O)C1=CC=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 9, 13, 9, 9, 9, 9, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 43, 63, 76, 76, 76, 76, 13, 13, 1, 9, 13, 13, 9, 9, 6, 1, 1, 1, 1, 13, 43, 43, 63, 63, 1, 1, 9] 201 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 43, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 314 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114088 none NC(=O)C1=CC=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 70, 89, 70, 70, 70, 70, 55, 55, 55, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 13, 70, 89, 89, 70, 70, 55, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13, 70] 201 rigid atoms, others: [37, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 283 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114088 none NC(=O)C1=CC=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 70, 70, 70, 134, 173, 174, 174, 174, 174, 70, 70, 9, 1, 3, 3, 1, 1, 3, 9, 9, 9, 9, 70, 134, 134, 173, 173, 9, 9, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 44, 27, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 648 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114088 none NC(=O)C1=CC=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 174, 201, 174, 174, 174, 174, 174, 174, 174, 77, 77, 77, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 77, 174, 201, 201, 174, 174, 174, 77, 77, 77, 77, 14, 6, 6, 4, 4, 77, 77, 174] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 583 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114088 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114088/1 /scratch/stefan/7770410/working/building/REAL300020114088 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1794) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1794 `/scratch/stefan/7770410/working/3D/1794' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CC=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020114088.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114088/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114088 none NC(=O)C1=CC=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 9, 13, 9, 9, 9, 9, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 43, 63, 76, 76, 76, 76, 13, 13, 1, 9, 13, 13, 9, 9, 6, 1, 1, 1, 1, 13, 43, 43, 63, 63, 1, 1, 9] 201 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 43, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 314 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114088 none NC(=O)C1=CC=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 70, 89, 70, 70, 70, 70, 55, 55, 55, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 13, 70, 89, 89, 70, 70, 55, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13, 70] 201 rigid atoms, others: [37, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 283 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114088 none NC(=O)C1=CC=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 70, 70, 70, 134, 173, 174, 174, 174, 174, 70, 70, 9, 1, 3, 3, 1, 1, 3, 9, 9, 9, 9, 70, 134, 134, 173, 173, 9, 9, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 44, 27, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 648 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114088 none NC(=O)C1=CC=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 174, 201, 174, 174, 174, 174, 174, 174, 174, 77, 77, 77, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 77, 174, 201, 201, 174, 174, 174, 77, 77, 77, 77, 14, 6, 6, 4, 4, 77, 77, 174] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 583 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114088 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114088 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114088/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114088/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114088 Building REAL300020114089 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114089' /scratch/stefan/7770410/working/building/REAL300020114089 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114089 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114089/0 /scratch/stefan/7770410/working/building/REAL300020114089 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1795) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1795 `/scratch/stefan/7770410/working/3D/1795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1) `REAL300020114089.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114089 none CC(C)C1=NC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 22, 67, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 35, 44, 60, 60, 60, 60, 7, 7, 1, 22, 67, 67, 67, 67, 67, 67, 67, 22, 6, 1, 1, 1, 1, 7, 35, 35, 44, 44, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 397 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114089 none CC(C)C1=NC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 60, 133, 60, 60, 60, 28, 28, 28, 7, 7, 7, 1, 1, 1, 1, 1, 8, 10, 15, 15, 15, 15, 1, 1, 7, 60, 133, 133, 133, 133, 133, 133, 133, 60, 28, 7, 7, 7, 7, 1, 8, 8, 10, 10, 7, 7] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 462 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114089 none CC(C)C1=NC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 1, 1, 1, 1, 1, 6, 6, 6, 22, 22, 22, 60, 60, 60, 133, 157, 185, 185, 185, 185, 60, 60, 22, 1, 10, 10, 10, 9, 10, 10, 10, 1, 6, 22, 22, 22, 22, 60, 133, 133, 157, 157, 22, 22] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 653 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114089 none CC(C)C1=NC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 186, 201, 186, 186, 186, 152, 152, 152, 68, 68, 68, 22, 22, 22, 7, 4, 1, 1, 1, 1, 1, 1, 22, 22, 68, 186, 201, 201, 201, 201, 201, 201, 201, 186, 152, 68, 68, 68, 68, 22, 7, 7, 4, 4, 68, 68] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 574 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114089 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114089/1 /scratch/stefan/7770410/working/building/REAL300020114089 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1796) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1796 `/scratch/stefan/7770410/working/3D/1796' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1) `REAL300020114089.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114089/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114089 none CC(C)C1=NC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 22, 66, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 37, 47, 62, 62, 62, 62, 7, 7, 1, 22, 66, 66, 66, 66, 66, 66, 66, 22, 6, 1, 1, 1, 1, 7, 37, 37, 47, 47, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 404 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114089 none CC(C)C1=NC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 60, 133, 60, 60, 60, 28, 28, 28, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 7, 60, 133, 133, 133, 133, 133, 133, 133, 60, 28, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 465 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114089 none CC(C)C1=NC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 1, 1, 1, 1, 1, 6, 6, 6, 22, 22, 22, 60, 60, 60, 133, 158, 183, 183, 183, 183, 60, 60, 22, 1, 11, 11, 11, 10, 11, 11, 11, 1, 6, 22, 22, 22, 22, 60, 133, 133, 158, 158, 22, 22] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 659 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114089 none CC(C)C1=NC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 186, 201, 186, 186, 186, 153, 153, 153, 69, 69, 69, 22, 22, 22, 7, 4, 1, 1, 1, 1, 1, 1, 22, 22, 69, 186, 201, 201, 201, 201, 201, 201, 201, 186, 153, 69, 69, 69, 69, 22, 7, 7, 4, 4, 69, 69] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 577 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114089 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114089 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114089/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114089/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114089 Building REAL300020114090 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114090' /scratch/stefan/7770410/working/building/REAL300020114090 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114090 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114090/0 /scratch/stefan/7770410/working/building/REAL300020114090 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1797) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1797 `/scratch/stefan/7770410/working/3D/1797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC2=C1OC(C(=O)NC1CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C1)C2) `REAL300020114090.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114090 none CC1=CC=CC2=C1OC(C(=O)NC1CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 43, 62, 76, 76, 76, 76, 11, 11, 1, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 43, 43, 62, 62, 1, 1, 22, 22] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49]) total number of confs: 334 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114090 none CC1=CC=CC2=C1OC(C(=O)NC1CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 104, 104, 104, 104, 104, 44, 44, 44, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 14, 14, 14, 14, 1, 1, 11, 104, 104, 104, 104, 104, 104, 104, 104, 44, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 104, 104] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 345 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114090 none CC1=CC=CC2=C1OC(C(=O)NC1CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 22, 22, 22, 104, 104, 104, 178, 201, 201, 201, 201, 201, 104, 104, 22, 1, 2, 2, 2, 1, 1, 1, 1, 6, 22, 22, 22, 22, 104, 178, 178, 201, 201, 22, 22, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 34, 48, 49, 35, 28, 5] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 664 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114090 none CC1=CC=CC2=C1OC(C(=O)NC1CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 182, 182, 182, 76, 76, 76, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 76, 201, 201, 201, 201, 201, 201, 201, 201, 182, 76, 76, 76, 76, 14, 6, 6, 4, 4, 76, 76, 201, 201] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 572 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114090 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114090/1 /scratch/stefan/7770410/working/building/REAL300020114090 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1798) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1798 `/scratch/stefan/7770410/working/3D/1798' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC2=C1OC(C(=O)NC1CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C1)C2) `REAL300020114090.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114090/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114090 none CC1=CC=CC2=C1OC(C(=O)NC1CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 43, 62, 76, 76, 76, 76, 11, 11, 1, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 43, 43, 62, 62, 1, 1, 22, 22] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49]) total number of confs: 334 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114090 none CC1=CC=CC2=C1OC(C(=O)NC1CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 104, 104, 104, 104, 104, 44, 44, 44, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 14, 14, 14, 14, 1, 1, 11, 104, 104, 104, 104, 104, 104, 104, 104, 44, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 104, 104] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 345 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114090 none CC1=CC=CC2=C1OC(C(=O)NC1CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 22, 22, 22, 104, 104, 104, 178, 201, 201, 201, 201, 201, 104, 104, 22, 1, 2, 2, 2, 1, 1, 1, 1, 6, 22, 22, 22, 22, 104, 178, 178, 201, 201, 22, 22, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 34, 48, 49, 35, 28, 5] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 664 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114090 none CC1=CC=CC2=C1OC(C(=O)NC1CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 182, 182, 182, 76, 76, 76, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 76, 201, 201, 201, 201, 201, 201, 201, 201, 182, 76, 76, 76, 76, 14, 6, 6, 4, 4, 76, 76, 201, 201] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 572 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114090 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114090 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114090/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114090/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114090 Building REAL300020114091 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114091' /scratch/stefan/7770410/working/building/REAL300020114091 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114091 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114091/0 /scratch/stefan/7770410/working/building/REAL300020114091 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1799) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1799 `/scratch/stefan/7770410/working/3D/1799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)C(=O)NCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114091.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114091 none CCC(CC)C(=O)NCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 98, 115, 115, 98, 98, 92, 22, 22, 22, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 98, 92, 92, 22, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [14, 47, 16, 17, 18, 25, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 479 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114091 none CCC(CC)C(=O)NCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 193, 69, 69, 69, 38, 38, 38, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 38, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 193, 193, 69, 38, 38, 38, 38, 9, 4, 4, 2, 2, 38, 38] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 730 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114091 none CCC(CC)C(=O)NCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 29, 40, 40, 29, 29, 25, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 24, 36, 36, 36, 36, 36, 8, 8, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 29, 25, 25, 5, 1, 1, 1, 1, 8, 24, 24, 36, 36, 1, 1] 201 rigid atoms, others: [11, 15, 44, 43, 12, 13, 14, 45, 52, 46, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 314 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114091 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114091/1 /scratch/stefan/7770410/working/building/REAL300020114091 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1800) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1800 `/scratch/stefan/7770410/working/3D/1800' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)C(=O)NCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114091.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114091/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114091 none CCC(CC)C(=O)NCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 98, 115, 115, 98, 98, 92, 22, 22, 22, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 98, 92, 92, 22, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [14, 47, 16, 17, 18, 25, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53]) total number of confs: 479 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114091 none CCC(CC)C(=O)NCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 193, 68, 68, 68, 37, 37, 37, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 37, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 193, 193, 68, 37, 37, 37, 37, 8, 4, 4, 2, 2, 37, 37] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 731 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114091 none CCC(CC)C(=O)NCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 29, 40, 40, 29, 29, 25, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 25, 37, 37, 37, 37, 37, 8, 8, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 29, 25, 25, 5, 1, 1, 1, 1, 8, 25, 25, 37, 37, 1, 1] 201 rigid atoms, others: [11, 15, 44, 43, 12, 13, 14, 45, 52, 46, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114091 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114091 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114091/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114091/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114091 Building REAL300020114092 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114092' /scratch/stefan/7770410/working/building/REAL300020114092 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114092 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114092/0 /scratch/stefan/7770410/working/building/REAL300020114092 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1801) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1801 `/scratch/stefan/7770410/working/3D/1801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC2CCC1C2) `REAL300020114092.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114092 none CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC2CCC1C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 50, 73, 84, 84, 84, 84, 12, 12, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 12, 50, 50, 73, 73, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 143 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 41, 40, 20, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 332 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114092 none CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC2CCC1C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 49, 12, 12, 12, 1, 1, 1, 1, 1, 9, 14, 17, 17, 17, 17, 1, 1, 12, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 12, 12, 12, 12, 1, 9, 9, 14, 14, 12, 12, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 143 rigid atoms, others: [35, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 184 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114092 none CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC2CCC1C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 2, 2, 2, 6, 6, 6, 49, 49, 49, 109, 143, 143, 143, 143, 143, 49, 49, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 6, 6, 6, 6, 49, 109, 109, 143, 143, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 143 rigid atoms, others: [0, 1, 2, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 21, 22, 23, 24, 25, 26] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 561 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114092 none CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CC2CCC1C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [145, 145, 145, 145, 87, 87, 87, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 87, 145, 145, 145, 145, 145, 145, 145, 145, 145, 145, 87, 87, 87, 87, 18, 6, 6, 4, 4, 87, 87, 145, 145, 145, 145, 145, 145, 145, 145, 145, 145] 145 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 399 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114092 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114092/1 /scratch/stefan/7770410/working/building/REAL300020114092 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1802) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1802 `/scratch/stefan/7770410/working/3D/1802' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC2CCC1C2) `REAL300020114092.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114092 none CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC2CCC1C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 51, 74, 87, 87, 87, 87, 12, 12, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 12, 51, 51, 74, 74, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 144 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 41, 40, 20, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 339 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114092 none CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC2CCC1C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 12, 12, 12, 1, 1, 1, 1, 1, 9, 14, 17, 17, 17, 17, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 9, 9, 14, 14, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 144 rigid atoms, others: [35, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 186 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114092 none CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC2CCC1C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 2, 2, 2, 6, 6, 6, 50, 50, 50, 109, 144, 144, 144, 144, 144, 50, 50, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 6, 6, 6, 6, 50, 109, 109, 144, 144, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 144 rigid atoms, others: [0, 1, 2, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 21, 22, 23, 24, 25, 26] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 565 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114092 none CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CC2CCC1C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [144, 144, 144, 144, 87, 87, 87, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 87, 144, 144, 144, 144, 144, 144, 144, 144, 144, 144, 87, 87, 87, 87, 18, 6, 6, 4, 4, 87, 87, 144, 144, 144, 144, 144, 144, 144, 144, 144, 144] 144 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 397 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114092 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114092 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114092/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114092/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114092 Building REAL300020114093 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114093' /scratch/stefan/7770410/working/building/REAL300020114093 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114093 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114093/0 /scratch/stefan/7770410/working/building/REAL300020114093 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1803) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1803 `/scratch/stefan/7770410/working/3D/1803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1C1=CC=CC=C1) `REAL300020114093.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114093 none CC1C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 37, 53, 62, 62, 62, 62, 11, 11, 1, 17, 17, 26, 26, 19, 26, 26, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 11, 37, 37, 53, 53, 1, 1, 17, 26, 26, 17, 26, 26] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 44, 45, 21, 38, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51]) total number of confs: 313 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114093 none CC1C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 9, 9, 9, 26, 26, 26, 102, 102, 102, 163, 201, 201, 201, 201, 201, 102, 102, 26, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 9, 26, 26, 26, 26, 102, 163, 163, 201, 201, 26, 26, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [47, 48, 49, 50, 51, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 715 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114093 none CC1C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 39, 39, 39, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 83, 83, 102, 102, 87, 102, 102, 83, 83, 83, 83, 83, 39, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 83, 102, 102, 83, 102, 102] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 362 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114093 none CC1C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 83, 83, 83, 155, 198, 201, 201, 201, 201, 83, 83, 17, 1, 1, 3, 3, 2, 3, 3, 2, 2, 2, 1, 1, 5, 17, 17, 17, 17, 83, 155, 155, 198, 198, 17, 17, 1, 3, 3, 2, 3, 3] 201 rigid atoms, others: [0, 1, 2, 3, 33, 32, 46, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51]) total number of confs: 759 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114093 none CC1C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 137, 137, 137, 63, 63, 63, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 63, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 137, 63, 63, 63, 63, 11, 6, 6, 4, 4, 63, 63, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 609 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114093 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114093/1 /scratch/stefan/7770410/working/building/REAL300020114093 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1804) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1804 `/scratch/stefan/7770410/working/3D/1804' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1C1=CC=CC=C1) `REAL300020114093.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114093/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114093 none CC1C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 37, 53, 62, 62, 62, 62, 11, 11, 1, 17, 17, 25, 25, 18, 25, 25, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 11, 37, 37, 53, 53, 1, 1, 17, 25, 25, 17, 25, 25] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 44, 45, 21, 38, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51]) total number of confs: 310 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114093 none CC1C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 9, 9, 9, 25, 25, 25, 101, 101, 101, 162, 201, 201, 201, 201, 201, 101, 101, 25, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 9, 25, 25, 25, 25, 101, 162, 162, 201, 201, 25, 25, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [47, 48, 49, 50, 51, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 719 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114093 none CC1C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 39, 39, 39, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 84, 84, 101, 101, 88, 101, 101, 84, 84, 84, 84, 84, 39, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 84, 101, 101, 84, 101, 101] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 354 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114093 none CC1C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 84, 84, 84, 155, 198, 201, 201, 201, 201, 84, 84, 17, 1, 1, 3, 3, 2, 3, 3, 2, 2, 2, 1, 1, 5, 17, 17, 17, 17, 84, 155, 155, 198, 198, 17, 17, 1, 3, 3, 2, 3, 3] 201 rigid atoms, others: [0, 1, 2, 3, 33, 32, 46, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51]) total number of confs: 754 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114093 none CC1C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 138, 138, 138, 63, 63, 63, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 63, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 138, 63, 63, 63, 63, 11, 6, 6, 4, 4, 63, 63, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 611 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114093 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114093 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114093/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114093/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114093 Building REAL300020114094 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114094' /scratch/stefan/7770410/working/building/REAL300020114094 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114094 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114094/0 /scratch/stefan/7770410/working/building/REAL300020114094 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1805) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1805 `/scratch/stefan/7770410/working/3D/1805' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C2=CC=CC=C21) `REAL300020114094.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114094 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 38, 49, 67, 67, 67, 67, 7, 7, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 6, 1, 1, 1, 1, 7, 38, 38, 49, 49, 1, 1, 33, 33, 33, 33] 201 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 43, 44, 22] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48]) total number of confs: 265 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114094 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 28, 28, 28, 7, 7, 7, 1, 1, 1, 1, 1, 8, 12, 18, 18, 18, 18, 1, 1, 7, 104, 104, 104, 104, 104, 104, 104, 104, 104, 104, 28, 7, 7, 7, 7, 1, 8, 8, 12, 12, 7, 7, 104, 104, 104, 104] 201 rigid atoms, others: [38, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 229 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114094 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 11, 11, 11, 33, 33, 33, 104, 104, 104, 185, 201, 201, 201, 201, 201, 104, 104, 33, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 11, 33, 33, 33, 33, 104, 185, 185, 201, 201, 33, 33, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 32, 45, 46, 47, 48, 23, 24, 25, 26, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 668 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114094 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 162, 162, 162, 77, 77, 77, 28, 28, 28, 7, 4, 1, 1, 1, 1, 1, 1, 28, 28, 77, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 162, 77, 77, 77, 77, 28, 7, 7, 4, 4, 77, 77, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 523 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114094 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114094/1 /scratch/stefan/7770410/working/building/REAL300020114094 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1806) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1806 `/scratch/stefan/7770410/working/3D/1806' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C2=CC=CC=C21) `REAL300020114094.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114094 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 37, 49, 65, 65, 65, 65, 7, 7, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 6, 1, 1, 1, 1, 7, 37, 37, 49, 49, 1, 1, 33, 33, 33, 33] 201 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 43, 44, 22] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48]) total number of confs: 264 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114094 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 28, 28, 28, 7, 7, 7, 1, 1, 1, 1, 1, 8, 12, 18, 18, 18, 18, 1, 1, 7, 103, 103, 103, 103, 103, 103, 103, 103, 103, 103, 28, 7, 7, 7, 7, 1, 8, 8, 12, 12, 7, 7, 103, 103, 103, 103] 201 rigid atoms, others: [38, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 228 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114094 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 11, 11, 11, 33, 33, 33, 103, 103, 103, 185, 201, 201, 201, 201, 201, 103, 103, 33, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 11, 33, 33, 33, 33, 103, 185, 185, 201, 201, 33, 33, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 32, 45, 46, 47, 48, 23, 24, 25, 26, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 673 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114094 none CN1C=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 161, 161, 161, 76, 76, 76, 29, 29, 29, 7, 4, 1, 1, 1, 1, 1, 1, 29, 29, 76, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 161, 76, 76, 76, 76, 29, 7, 7, 4, 4, 76, 76, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 522 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114094 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114094 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114094/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114094/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114094 Building REAL300020114095 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114095' /scratch/stefan/7770410/working/building/REAL300020114095 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114095 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114095/0 /scratch/stefan/7770410/working/building/REAL300020114095 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1807) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1807 `/scratch/stefan/7770410/working/3D/1807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C(C)S1) `REAL300020114095.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114095 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 22, 30, 35, 35, 35, 35, 5, 5, 1, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 5, 22, 22, 30, 30, 1, 1, 20, 20, 20] 72 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 40, 22, 41, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 158 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114095 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 19, 19, 19, 5, 5, 5, 1, 1, 1, 1, 1, 8, 11, 14, 14, 14, 14, 1, 1, 5, 39, 39, 39, 39, 39, 39, 39, 19, 5, 5, 5, 5, 1, 8, 8, 11, 11, 5, 5, 39, 39, 39] 72 rigid atoms, others: [35, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 126 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114095 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 20, 20, 20, 39, 39, 39, 63, 72, 72, 72, 72, 72, 39, 39, 20, 1, 1, 1, 2, 2, 2, 1, 7, 20, 20, 20, 20, 39, 63, 63, 72, 72, 20, 20, 2, 2, 2] 72 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114095 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 52, 52, 52, 36, 36, 36, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 36, 72, 72, 72, 72, 72, 72, 72, 52, 36, 36, 36, 36, 15, 6, 6, 4, 4, 36, 36, 72, 72, 72] 72 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 188 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114095 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114095/1 /scratch/stefan/7770410/working/building/REAL300020114095 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1808) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1808 `/scratch/stefan/7770410/working/3D/1808' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C(C)S1) `REAL300020114095.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114095 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 22, 30, 35, 35, 35, 35, 5, 5, 1, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 5, 22, 22, 30, 30, 1, 1, 20, 20, 20] 71 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 40, 22, 41, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 158 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114095 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 19, 19, 19, 5, 5, 5, 1, 1, 1, 1, 1, 8, 11, 14, 14, 14, 14, 1, 1, 5, 39, 39, 39, 39, 39, 39, 39, 19, 5, 5, 5, 5, 1, 8, 8, 11, 11, 5, 5, 39, 39, 39] 71 rigid atoms, others: [35, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 126 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114095 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 20, 20, 20, 39, 39, 39, 63, 71, 71, 71, 71, 71, 39, 39, 20, 1, 1, 1, 2, 2, 2, 1, 7, 20, 20, 20, 20, 39, 63, 63, 71, 71, 20, 20, 2, 2, 2] 71 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114095 none CC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 52, 52, 52, 36, 36, 36, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 36, 71, 71, 71, 71, 71, 71, 71, 52, 36, 36, 36, 36, 15, 6, 6, 4, 4, 36, 36, 71, 71, 71] 71 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 186 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114095 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114095 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114095/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114095/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114095 Building REAL300020114096 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114096' /scratch/stefan/7770410/working/building/REAL300020114096 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114096 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114096/0 /scratch/stefan/7770410/working/building/REAL300020114096 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1809) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1809 `/scratch/stefan/7770410/working/3D/1809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)NCCCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114096.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114096 none NC(=O)NCCCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [123, 123, 123, 122, 89, 83, 70, 14, 14, 14, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 123, 123, 123, 122, 122, 89, 89, 89, 89, 70, 70, 14, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 604 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114096 none NC(=O)NCCCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 200, 158, 149, 139, 35, 35, 35, 28, 28, 28, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 28, 201, 201, 201, 200, 200, 158, 158, 158, 158, 139, 139, 35, 28, 28, 28, 28, 8, 4, 4, 2, 2, 28, 28] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 891 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114096 none NC(=O)NCCCCC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 57, 29, 26, 20, 4, 4, 4, 1, 1, 1, 1, 1, 7, 7, 7, 19, 29, 29, 29, 29, 29, 7, 7, 1, 58, 58, 58, 57, 57, 29, 29, 29, 29, 20, 20, 4, 1, 1, 1, 1, 7, 19, 19, 29, 29, 1, 1] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 398 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114096 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114096/1 /scratch/stefan/7770410/working/building/REAL300020114096 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1810) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1810 `/scratch/stefan/7770410/working/3D/1810' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)NCCCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114096.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114096 none NC(=O)NCCCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [123, 123, 123, 122, 89, 83, 70, 14, 14, 14, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 123, 123, 123, 122, 122, 89, 89, 89, 89, 70, 70, 14, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 604 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114096 none NC(=O)NCCCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 200, 157, 148, 138, 35, 35, 35, 28, 28, 28, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 28, 201, 201, 201, 200, 200, 157, 157, 157, 157, 138, 138, 35, 28, 28, 28, 28, 8, 4, 4, 2, 2, 28, 28] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 891 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114096 none NC(=O)NCCCCC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 57, 29, 26, 20, 4, 4, 4, 1, 1, 1, 1, 1, 7, 7, 7, 19, 29, 29, 29, 29, 29, 7, 7, 1, 58, 58, 58, 57, 57, 29, 29, 29, 29, 20, 20, 4, 1, 1, 1, 1, 7, 19, 19, 29, 29, 1, 1] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 398 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114096 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114096 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114096/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114096/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114096 Building REAL300020114097 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114097' /scratch/stefan/7770410/working/building/REAL300020114097 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114097 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114097/0 /scratch/stefan/7770410/working/building/REAL300020114097 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1811) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1811 `/scratch/stefan/7770410/working/3D/1811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1) `REAL300020114097.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114097 none CCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 36, 51, 61, 61, 61, 61, 11, 11, 1, 11, 21, 21, 21, 21, 21, 11, 11, 6, 1, 1, 1, 1, 11, 36, 36, 51, 51, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 303 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114097 none CCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 43, 43, 43, 43, 36, 36, 36, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 43, 82, 82, 82, 82, 82, 43, 43, 36, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 378 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114097 none CCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 43, 43, 43, 85, 118, 121, 121, 121, 121, 43, 43, 11, 1, 4, 4, 4, 3, 3, 1, 1, 4, 11, 11, 11, 11, 43, 85, 85, 118, 118, 11, 11] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 25, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 494 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114097 none CCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 125, 125, 125, 125, 123, 123, 123, 62, 62, 62, 14, 14, 14, 7, 4, 1, 1, 1, 1, 1, 1, 14, 14, 62, 125, 201, 201, 201, 201, 201, 125, 125, 123, 62, 62, 62, 62, 14, 7, 7, 4, 4, 62, 62] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 803 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114097 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114097/1 /scratch/stefan/7770410/working/building/REAL300020114097 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1812) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1812 `/scratch/stefan/7770410/working/3D/1812' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1) `REAL300020114097.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114097 none CCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 36, 51, 61, 61, 61, 61, 11, 11, 1, 11, 21, 21, 21, 21, 21, 11, 11, 6, 1, 1, 1, 1, 11, 36, 36, 51, 51, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 303 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114097 none CCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 43, 43, 43, 43, 36, 36, 36, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 43, 82, 82, 82, 82, 82, 43, 43, 36, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 378 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114097 none CCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 43, 43, 43, 85, 118, 121, 121, 121, 121, 43, 43, 11, 1, 4, 4, 4, 3, 3, 1, 1, 4, 11, 11, 11, 11, 43, 85, 85, 118, 118, 11, 11] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 25, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 494 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114097 none CCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 125, 125, 125, 125, 123, 123, 123, 62, 62, 62, 14, 14, 14, 7, 4, 1, 1, 1, 1, 1, 1, 14, 14, 62, 125, 201, 201, 201, 201, 201, 125, 125, 123, 62, 62, 62, 62, 14, 7, 7, 4, 4, 62, 62] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 803 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114097 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114097 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114097/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114097/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114097 Building REAL300020114098 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114098' /scratch/stefan/7770410/working/building/REAL300020114098 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114098 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114098/0 /scratch/stefan/7770410/working/building/REAL300020114098 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1813) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1813 `/scratch/stefan/7770410/working/3D/1813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C)C=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114098.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114098 none COC1=CC=C(C)C=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 26, 26, 26, 26, 26, 26, 26, 24, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 33, 46, 48, 48, 48, 48, 10, 10, 1, 35, 35, 35, 26, 26, 26, 26, 26, 26, 24, 24, 6, 1, 1, 1, 1, 10, 33, 33, 46, 46, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 286 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114098 none COC1=CC=C(C)C=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 95, 95, 95, 95, 95, 95, 95, 92, 29, 29, 29, 10, 10, 10, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 10, 104, 104, 104, 95, 95, 95, 95, 95, 95, 92, 92, 29, 10, 10, 10, 10, 1, 8, 8, 10, 10, 10, 10] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 395 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114098 none COC1=CC=C(C)C=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 26, 26, 26, 95, 95, 95, 167, 199, 201, 201, 201, 201, 95, 95, 26, 3, 3, 3, 1, 1, 2, 2, 2, 1, 5, 5, 11, 26, 26, 26, 26, 95, 167, 167, 199, 199, 26, 26] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 8, 9, 7, 37] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 729 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114098 none COC1=CC=C(C)C=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 199, 101, 101, 101, 48, 48, 48, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 48, 201, 201, 201, 201, 201, 201, 201, 201, 201, 199, 199, 101, 48, 48, 48, 48, 13, 6, 6, 4, 4, 48, 48] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 730 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114098 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114098/1 /scratch/stefan/7770410/working/building/REAL300020114098 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1814) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1814 `/scratch/stefan/7770410/working/3D/1814' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C)C=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114098.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114098/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114098 none COC1=CC=C(C)C=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 26, 26, 26, 26, 26, 26, 26, 24, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 32, 45, 47, 47, 47, 47, 10, 10, 1, 34, 34, 34, 26, 26, 26, 26, 26, 26, 24, 24, 6, 1, 1, 1, 1, 10, 32, 32, 45, 45, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 281 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114098 none COC1=CC=C(C)C=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 94, 94, 94, 94, 94, 94, 94, 92, 29, 29, 29, 10, 10, 10, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 10, 104, 104, 104, 94, 94, 94, 94, 94, 94, 92, 92, 29, 10, 10, 10, 10, 1, 8, 8, 10, 10, 10, 10] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 395 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114098 none COC1=CC=C(C)C=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 26, 26, 26, 94, 94, 94, 167, 199, 201, 201, 201, 201, 94, 94, 26, 3, 3, 3, 1, 1, 2, 2, 2, 1, 5, 5, 11, 26, 26, 26, 26, 94, 167, 167, 199, 199, 26, 26] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 8, 9, 7, 37] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 733 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114098 none COC1=CC=C(C)C=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 199, 102, 102, 102, 49, 49, 49, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 49, 201, 201, 201, 201, 201, 201, 201, 201, 201, 199, 199, 102, 49, 49, 49, 49, 13, 6, 6, 4, 4, 49, 49] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 729 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114098 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114098 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114098/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114098/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114098 Building REAL300020114099 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114099' /scratch/stefan/7770410/working/building/REAL300020114099 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114099 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114099/0 /scratch/stefan/7770410/working/building/REAL300020114099 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1815) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1815 `/scratch/stefan/7770410/working/3D/1815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1) `REAL300020114099.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114099 none CC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 19, 22, 22, 16, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 29, 42, 46, 46, 46, 46, 11, 11, 1, 22, 22, 22, 22, 22, 22, 22, 16, 16, 6, 1, 1, 1, 1, 11, 29, 29, 42, 42, 1, 1, 22, 22] 201 rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 11, 12, 45, 44, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47]) total number of confs: 257 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114099 none CC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 81, 87, 87, 73, 33, 33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 87, 87, 87, 87, 87, 87, 87, 73, 73, 33, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 87, 87] 201 rigid atoms, others: [39, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 341 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114099 none CC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 24, 24, 24, 88, 88, 88, 156, 201, 201, 201, 201, 201, 88, 88, 24, 1, 1, 2, 2, 2, 1, 1, 5, 5, 9, 24, 24, 24, 24, 88, 156, 156, 201, 201, 24, 24, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 46, 47, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 768 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114099 none CC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 101, 101, 101, 49, 49, 49, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 49, 201, 201, 201, 201, 201, 201, 201, 201, 201, 101, 49, 49, 49, 49, 11, 6, 6, 4, 4, 49, 49, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 725 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114099 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114099/1 /scratch/stefan/7770410/working/building/REAL300020114099 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1816) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1816 `/scratch/stefan/7770410/working/3D/1816' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1) `REAL300020114099.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114099/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114099 none CC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 19, 22, 22, 16, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 29, 42, 47, 47, 47, 47, 11, 11, 1, 22, 22, 22, 22, 22, 22, 22, 16, 16, 6, 1, 1, 1, 1, 11, 29, 29, 42, 42, 1, 1, 22, 22] 201 rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 11, 12, 45, 44, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47]) total number of confs: 259 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114099 none CC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 81, 87, 87, 74, 33, 33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 87, 87, 87, 87, 87, 87, 87, 74, 74, 33, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 87, 87] 201 rigid atoms, others: [39, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 345 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114099 none CC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 24, 24, 24, 89, 89, 89, 157, 201, 201, 201, 201, 201, 89, 89, 24, 1, 1, 2, 2, 2, 1, 1, 5, 5, 9, 24, 24, 24, 24, 89, 157, 157, 201, 201, 24, 24, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 46, 47, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 763 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114099 none CC1=CC=C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 101, 101, 101, 49, 49, 49, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 49, 201, 201, 201, 201, 201, 201, 201, 201, 201, 101, 49, 49, 49, 49, 11, 6, 6, 4, 4, 49, 49, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 725 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114099 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114099 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114099/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114099/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114099 Building REAL300020114100 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114100' /scratch/stefan/7770410/working/building/REAL300020114100 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114100 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114100/0 /scratch/stefan/7770410/working/building/REAL300020114100 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1817) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1817 `/scratch/stefan/7770410/working/3D/1817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SN=N1) `REAL300020114100.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114100 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [39, 27, 27, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 18, 26, 28, 28, 28, 28, 6, 6, 1, 27, 27, 27, 39, 39, 39, 39, 39, 6, 1, 1, 1, 1, 6, 18, 18, 26, 26, 1, 1] 91 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40]) total number of confs: 208 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114100 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [59, 45, 45, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 6, 45, 45, 45, 59, 59, 59, 59, 59, 20, 6, 6, 6, 6, 1, 7, 7, 9, 9, 6, 6] 91 rigid atoms, others: [36, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 197 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114100 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 11, 11, 11, 27, 27, 27, 45, 45, 45, 68, 81, 83, 83, 83, 83, 45, 45, 27, 1, 1, 1, 6, 6, 6, 6, 6, 11, 27, 27, 27, 27, 45, 68, 68, 81, 81, 27, 27] 91 rigid atoms, others: [1, 2, 3, 4, 23, 24, 25] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 303 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114100 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)SN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [92, 84, 84, 58, 58, 58, 31, 31, 31, 13, 13, 13, 8, 4, 1, 1, 1, 1, 1, 1, 13, 13, 31, 84, 84, 84, 92, 92, 92, 92, 92, 58, 31, 31, 31, 31, 13, 8, 8, 4, 4, 31, 31] 92 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 273 number of broken/clashed sets: 2 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114100 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114100/1 /scratch/stefan/7770410/working/building/REAL300020114100 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1818) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1818 `/scratch/stefan/7770410/working/3D/1818' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SN=N1) `REAL300020114100.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114100/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114100 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [38, 27, 27, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 18, 26, 28, 28, 28, 28, 6, 6, 1, 27, 27, 27, 38, 38, 38, 38, 38, 6, 1, 1, 1, 1, 6, 18, 18, 26, 26, 1, 1] 90 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40]) total number of confs: 202 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114100 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [58, 45, 45, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 6, 45, 45, 45, 58, 58, 58, 58, 58, 20, 6, 6, 6, 6, 1, 7, 7, 9, 9, 6, 6] 90 rigid atoms, others: [36, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 191 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114100 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 11, 11, 11, 27, 27, 27, 45, 45, 45, 68, 80, 82, 82, 82, 82, 45, 45, 27, 1, 1, 1, 6, 6, 6, 6, 6, 11, 27, 27, 27, 27, 45, 68, 68, 80, 80, 27, 27] 90 rigid atoms, others: [1, 2, 3, 4, 23, 24, 25] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 297 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114100 none CCC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)SN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 14, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [90, 82, 82, 57, 57, 57, 30, 30, 30, 13, 13, 13, 8, 4, 1, 1, 1, 1, 1, 1, 13, 13, 30, 82, 82, 82, 90, 90, 90, 90, 90, 57, 30, 30, 30, 30, 13, 8, 8, 4, 4, 30, 30] 90 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 269 number of broken/clashed sets: 2 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114100 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114100 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114100/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114100/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114100 Building REAL300020114101 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114101' /scratch/stefan/7770410/working/building/REAL300020114101 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114101 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114101/0 /scratch/stefan/7770410/working/building/REAL300020114101 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1819) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1819 `/scratch/stefan/7770410/working/3D/1819' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NC2=CC=CC=C21) `REAL300020114101.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114101 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 30, 88, 88, 88, 88, 88, 88, 88, 88, 88, 30, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 88, 88, 88, 88, 88, 88] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 184 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114101 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 45, 45, 45, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 45, 81, 201, 201, 201, 201, 201, 201, 201, 201, 201, 81, 45, 45, 45, 45, 10, 5, 5, 3, 3, 45, 45, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 399 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114101 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 45, 46, 46, 46, 46, 11, 11, 1, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 11, 31, 31, 45, 45, 1, 1, 20, 20, 20, 20, 20, 20] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114101 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 20, 20, 20, 88, 88, 88, 159, 201, 201, 201, 201, 201, 88, 88, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 20, 20, 20, 20, 88, 159, 159, 201, 201, 20, 20, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 764 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114101 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114101/1 /scratch/stefan/7770410/working/building/REAL300020114101 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1820) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1820 `/scratch/stefan/7770410/working/3D/1820' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NC2=CC=CC=C21) `REAL300020114101.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114101/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114101 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 30, 88, 88, 88, 88, 88, 88, 88, 88, 88, 30, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 88, 88, 88, 88, 88, 88] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 183 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114101 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 48, 48, 48, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 48, 83, 201, 201, 201, 201, 201, 201, 201, 201, 201, 83, 48, 48, 48, 48, 10, 5, 5, 3, 3, 48, 48, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 402 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114101 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 45, 46, 46, 46, 46, 11, 11, 1, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 11, 31, 31, 45, 45, 1, 1, 20, 20, 20, 20, 20, 20] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114101 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 20, 20, 20, 88, 88, 88, 158, 201, 201, 201, 201, 201, 88, 88, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 20, 20, 20, 20, 88, 158, 158, 201, 201, 20, 20, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 767 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114101 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114101 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114101/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114101/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114101 Building REAL300020114102 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114102' /scratch/stefan/7770410/working/building/REAL300020114102 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114102 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114102/0 /scratch/stefan/7770410/working/building/REAL300020114102 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1821) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1821 `/scratch/stefan/7770410/working/3D/1821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114102.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114102 none COC1=CC=C(C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 42, 42, 42, 12, 42, 42, 42, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 27, 36, 45, 45, 45, 45, 7, 7, 1, 60, 60, 60, 42, 42, 42, 42, 42, 42, 6, 1, 1, 1, 1, 7, 27, 27, 36, 36, 1, 1] 201 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 331 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114102 none COC1=CC=C(C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 94, 94, 94, 48, 94, 94, 94, 22, 22, 22, 7, 7, 7, 1, 1, 1, 1, 1, 8, 11, 14, 14, 14, 14, 1, 1, 7, 111, 111, 111, 94, 94, 94, 94, 94, 94, 22, 7, 7, 7, 7, 1, 8, 8, 11, 11, 7, 7] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 376 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114102 none COC1=CC=C(C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 42, 42, 42, 94, 94, 94, 177, 195, 201, 201, 201, 201, 94, 94, 42, 4, 4, 4, 1, 1, 2, 2, 2, 1, 11, 42, 42, 42, 42, 94, 177, 177, 195, 195, 42, 42] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 36, 31] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 730 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114102 none COC1=CC=C(C)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 192, 201, 201, 201, 93, 93, 93, 50, 50, 50, 19, 19, 19, 7, 4, 1, 1, 1, 1, 1, 1, 19, 19, 50, 201, 201, 201, 201, 201, 201, 201, 201, 201, 93, 50, 50, 50, 50, 19, 7, 7, 4, 4, 50, 50] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 483 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114102 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114102/1 /scratch/stefan/7770410/working/building/REAL300020114102 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1822) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1822 `/scratch/stefan/7770410/working/3D/1822' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114102.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114102 none COC1=CC=C(C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 42, 42, 42, 12, 42, 42, 42, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 27, 36, 45, 45, 45, 45, 7, 7, 1, 60, 60, 60, 42, 42, 42, 42, 42, 42, 6, 1, 1, 1, 1, 7, 27, 27, 36, 36, 1, 1] 201 rigid atoms, others: [47, 38, 39, 40, 41, 11, 12, 13, 14, 15, 48, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 331 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114102 none COC1=CC=C(C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 95, 95, 95, 48, 95, 95, 95, 22, 22, 22, 7, 7, 7, 1, 1, 1, 1, 1, 8, 11, 14, 14, 14, 14, 1, 1, 7, 112, 112, 112, 95, 95, 95, 95, 95, 95, 22, 7, 7, 7, 7, 1, 8, 8, 11, 11, 7, 7] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 376 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114102 none COC1=CC=C(C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 42, 42, 42, 95, 95, 95, 176, 194, 201, 201, 201, 201, 95, 95, 42, 4, 4, 4, 1, 1, 2, 2, 2, 1, 11, 42, 42, 42, 42, 95, 176, 176, 194, 194, 42, 42] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 36, 31] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 721 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114102 none COC1=CC=C(C)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 191, 201, 201, 201, 93, 93, 93, 50, 50, 50, 19, 19, 19, 7, 4, 1, 1, 1, 1, 1, 1, 19, 19, 50, 201, 201, 201, 201, 201, 201, 201, 201, 201, 93, 50, 50, 50, 50, 19, 7, 7, 4, 4, 50, 50] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 485 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114102 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114102 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114102/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114102/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114102 Building REAL300020114103 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114103' /scratch/stefan/7770410/working/building/REAL300020114103 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114103 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114103/0 /scratch/stefan/7770410/working/building/REAL300020114103 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1823) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1823 `/scratch/stefan/7770410/working/3D/1823' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCS(=O)(=O)C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114103.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114103 none O=C(CC1CCS(=O)(=O)C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 14, 11, 11, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 41, 70, 70, 70, 70, 70, 68, 1, 1, 1, 1, 1, 12, 12, 12, 13, 13, 13, 13, 13, 13, 12, 12, 1, 41, 41, 70, 70, 70, 70, 70, 70, 70, 6, 1, 1, 1, 1, 12, 13, 13, 13, 13, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 263 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114103 none O=C(CC1CCS(=O)(=O)C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 14, 11, 11, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 161, 201, 201, 201, 201, 201, 200, 12, 12, 12, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 12, 161, 161, 201, 201, 201, 201, 201, 201, 201, 42, 12, 12, 12, 12, 1, 3, 3, 3, 3, 12, 12] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 741 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114103 none O=C(CC1CCS(=O)(=O)C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 14, 11, 11, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 7, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 70, 70, 70, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 70, 7, 7, 1, 1, 1, 1, 1, 1, 1, 26, 70, 70, 70, 70, 201, 201, 201, 201, 201, 70, 70] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 371 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114103 none O=C(CC1CCS(=O)(=O)C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 14, 11, 11, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 161, 201, 201, 201, 201, 201, 200, 13, 13, 13, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 161, 161, 201, 201, 201, 201, 201, 201, 201, 41, 13, 13, 13, 13, 3, 3, 3, 1, 1, 13, 13] 201 rigid atoms, others: [44, 45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47]) total number of confs: 739 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114103 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114103/1 /scratch/stefan/7770410/working/building/REAL300020114103 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1824) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1824 `/scratch/stefan/7770410/working/3D/1824' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCS(=O)(=O)C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114103.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114103 none O=C(CC1CCS(=O)(=O)C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 14, 11, 11, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 41, 70, 70, 70, 70, 70, 68, 1, 1, 1, 1, 1, 12, 12, 12, 13, 13, 13, 13, 13, 13, 12, 12, 1, 41, 41, 70, 70, 70, 70, 70, 70, 70, 6, 1, 1, 1, 1, 12, 13, 13, 13, 13, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 263 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114103 none O=C(CC1CCS(=O)(=O)C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 14, 11, 11, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 161, 201, 201, 201, 201, 201, 200, 12, 12, 12, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 12, 161, 161, 201, 201, 201, 201, 201, 201, 201, 42, 12, 12, 12, 12, 1, 3, 3, 3, 3, 12, 12] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 741 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114103 none O=C(CC1CCS(=O)(=O)C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 14, 11, 11, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 7, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 70, 70, 70, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 70, 7, 7, 1, 1, 1, 1, 1, 1, 1, 26, 70, 70, 70, 70, 201, 201, 201, 201, 201, 70, 70] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 371 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114103 none O=C(CC1CCS(=O)(=O)C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 14, 11, 11, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 161, 201, 201, 201, 201, 201, 200, 13, 13, 13, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 161, 161, 201, 201, 201, 201, 201, 201, 201, 41, 13, 13, 13, 13, 3, 3, 3, 1, 1, 13, 13] 201 rigid atoms, others: [44, 45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47]) total number of confs: 739 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114103 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114103 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114103/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114103/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114103 Building REAL300020114104 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114104' /scratch/stefan/7770410/working/building/REAL300020114104 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114104 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114104/0 /scratch/stefan/7770410/working/building/REAL300020114104 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1825) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1825 `/scratch/stefan/7770410/working/3D/1825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=NOC2=CC=CC=C21)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114104.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114104 none O=C(CC1=NOC2=CC=CC=C21)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 12, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 21, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 36, 36, 36, 36, 8, 8, 1, 21, 21, 27, 27, 27, 27, 5, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1] 201 rigid atoms, others: [45, 36, 37, 38, 39, 12, 13, 14, 15, 16, 46, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 228 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114104 none O=C(CC1=NOC2=CC=CC=C21)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 12, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 74, 98, 98, 98, 98, 98, 98, 98, 98, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 8, 8, 8, 8, 1, 1, 8, 74, 74, 98, 98, 98, 98, 23, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [40, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 340 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114104 none O=C(CC1=NOC2=CC=CC=C21)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 12, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 27, 27, 27, 98, 98, 98, 161, 201, 201, 201, 201, 201, 98, 98, 27, 4, 4, 1, 1, 1, 1, 11, 27, 27, 27, 27, 98, 161, 161, 201, 201, 27, 27] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 750 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114104 none O=C(CC1=NOC2=CC=CC=C21)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 12, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 145, 201, 201, 201, 201, 201, 201, 201, 201, 37, 37, 37, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 37, 145, 145, 201, 201, 201, 201, 70, 37, 37, 37, 37, 9, 5, 5, 3, 3, 37, 37] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 665 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114104 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114104/1 /scratch/stefan/7770410/working/building/REAL300020114104 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1826) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1826 `/scratch/stefan/7770410/working/3D/1826' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=NOC2=CC=CC=C21)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114104.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114104/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114104 none O=C(CC1=NOC2=CC=CC=C21)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 12, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 21, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 36, 36, 36, 36, 8, 8, 1, 21, 21, 27, 27, 27, 27, 5, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1] 201 rigid atoms, others: [45, 36, 37, 38, 39, 12, 13, 14, 15, 16, 46, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 228 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114104 none O=C(CC1=NOC2=CC=CC=C21)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 12, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 74, 98, 98, 98, 98, 98, 98, 98, 98, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 8, 8, 8, 8, 1, 1, 8, 74, 74, 98, 98, 98, 98, 23, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [40, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 340 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114104 none O=C(CC1=NOC2=CC=CC=C21)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 12, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 27, 27, 27, 98, 98, 98, 160, 201, 201, 201, 201, 201, 98, 98, 27, 4, 4, 1, 1, 1, 1, 11, 27, 27, 27, 27, 98, 160, 160, 201, 201, 27, 27] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 747 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114104 none O=C(CC1=NOC2=CC=CC=C21)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 12, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 145, 201, 201, 201, 201, 201, 201, 201, 201, 37, 37, 37, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 37, 145, 145, 201, 201, 201, 201, 70, 37, 37, 37, 37, 9, 5, 5, 3, 3, 37, 37] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 665 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114104 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114104 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114104/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114104/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114104 Building REAL300020114105 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114105' /scratch/stefan/7770410/working/building/REAL300020114105 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114105 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114105/0 /scratch/stefan/7770410/working/building/REAL300020114105 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1827) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1827 `/scratch/stefan/7770410/working/3D/1827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCN1C(=O)CCC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114105.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114105 none O=C(CCN1C(=O)CCC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 39, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 1, 11, 11, 11, 33, 48, 49, 49, 49, 49, 11, 11, 1, 39, 39, 42, 42, 42, 42, 42, 42, 6, 1, 1, 1, 1, 11, 33, 33, 48, 48, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 341 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114105 none O=C(CCN1C(=O)CCC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 124, 132, 132, 132, 132, 132, 132, 132, 11, 11, 11, 1, 1, 1, 1, 1, 5, 7, 8, 8, 8, 8, 1, 1, 11, 124, 124, 132, 132, 132, 132, 132, 132, 39, 11, 11, 11, 11, 1, 5, 5, 7, 7, 11, 11] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 513 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114105 none O=C(CCN1C(=O)CCC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 43, 43, 43, 130, 130, 130, 184, 201, 201, 201, 201, 201, 130, 130, 43, 5, 5, 5, 5, 1, 1, 1, 1, 14, 43, 43, 43, 43, 130, 184, 184, 201, 201, 43, 43] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 35] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 615 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114105 none O=C(CCN1C(=O)CCC1=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [122, 122, 122, 201, 201, 201, 201, 201, 201, 201, 201, 51, 51, 51, 9, 9, 9, 6, 4, 1, 1, 1, 1, 1, 1, 9, 9, 51, 201, 201, 201, 201, 201, 201, 201, 201, 122, 51, 51, 51, 51, 9, 6, 6, 4, 4, 51, 51] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 752 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114105 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114105/1 /scratch/stefan/7770410/working/building/REAL300020114105 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1828) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1828 `/scratch/stefan/7770410/working/3D/1828' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCN1C(=O)CCC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114105.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114105 none O=C(CCN1C(=O)CCC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 39, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 1, 11, 11, 11, 33, 48, 49, 49, 49, 49, 11, 11, 1, 39, 39, 42, 42, 42, 42, 42, 42, 6, 1, 1, 1, 1, 11, 33, 33, 48, 48, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 341 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114105 none O=C(CCN1C(=O)CCC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 124, 132, 132, 132, 132, 132, 132, 132, 11, 11, 11, 1, 1, 1, 1, 1, 5, 7, 8, 8, 8, 8, 1, 1, 11, 124, 124, 132, 132, 132, 132, 132, 132, 39, 11, 11, 11, 11, 1, 5, 5, 7, 7, 11, 11] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 513 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114105 none O=C(CCN1C(=O)CCC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 43, 43, 43, 130, 130, 130, 184, 201, 201, 201, 201, 201, 130, 130, 43, 5, 5, 5, 5, 1, 1, 1, 1, 14, 43, 43, 43, 43, 130, 184, 184, 201, 201, 43, 43] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 35] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 615 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114105 none O=C(CCN1C(=O)CCC1=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [122, 122, 122, 201, 201, 201, 201, 201, 201, 201, 201, 51, 51, 51, 9, 9, 9, 6, 4, 1, 1, 1, 1, 1, 1, 9, 9, 51, 201, 201, 201, 201, 201, 201, 201, 201, 122, 51, 51, 51, 51, 9, 6, 6, 4, 4, 51, 51] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 752 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114105 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114105 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114105/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114105/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114105 Building REAL300020114106 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114106' /scratch/stefan/7770410/working/building/REAL300020114106 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114106 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114106/0 /scratch/stefan/7770410/working/building/REAL300020114106 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1829) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1829 `/scratch/stefan/7770410/working/3D/1829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCS(=O)(=O)C1) `REAL300020114106.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114106 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 14, 11, 11, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 30, 96, 96, 96, 96, 96, 96, 30, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 96, 96, 96, 96, 96, 96, 96] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 283 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114106 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 14, 11, 11, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 51, 51, 51, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 51, 94, 201, 201, 201, 201, 201, 201, 94, 51, 51, 51, 51, 10, 6, 6, 4, 4, 51, 51, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 613 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114106 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 14, 11, 11, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 30, 44, 51, 51, 51, 51, 11, 11, 1, 6, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 11, 30, 30, 44, 44, 1, 1, 24, 24, 24, 24, 24, 24, 24] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114106 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 14, 11, 11, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 24, 24, 24, 96, 96, 96, 155, 201, 201, 201, 201, 201, 96, 96, 24, 1, 1, 1, 1, 1, 1, 1, 9, 24, 24, 24, 24, 96, 155, 155, 201, 201, 24, 24, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 38, 39, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 749 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114106 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114106/1 /scratch/stefan/7770410/working/building/REAL300020114106 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1830) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1830 `/scratch/stefan/7770410/working/3D/1830' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCS(=O)(=O)C1) `REAL300020114106.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114106 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 14, 11, 11, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 30, 97, 97, 97, 97, 97, 97, 30, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 97, 97, 97, 97, 97, 97, 97] 201 rigid atoms, others: [5, 6, 7, 8, 9, 16, 17, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 285 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114106 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 14, 11, 11, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 51, 51, 51, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 51, 94, 201, 201, 201, 201, 201, 201, 94, 51, 51, 51, 51, 10, 6, 6, 4, 4, 51, 51, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 613 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114106 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 14, 11, 11, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 30, 44, 51, 51, 51, 51, 11, 11, 1, 6, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 11, 30, 30, 44, 44, 1, 1, 24, 24, 24, 24, 24, 24, 24] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114106 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 14, 11, 11, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 24, 24, 24, 97, 97, 97, 156, 201, 201, 201, 201, 201, 97, 97, 24, 1, 1, 1, 1, 1, 1, 1, 9, 24, 24, 24, 24, 97, 156, 156, 201, 201, 24, 24, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 38, 39, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 744 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114106 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114106 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114106/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114106/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114106 Building REAL300020114107 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114107' /scratch/stefan/7770410/working/building/REAL300020114107 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114107 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114107/0 /scratch/stefan/7770410/working/building/REAL300020114107 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1831) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1831 `/scratch/stefan/7770410/working/3D/1831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1) `REAL300020114107.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114107 none CC(=O)N1CCCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 19, 30, 19, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 29, 43, 46, 46, 46, 46, 11, 11, 1, 19, 30, 30, 30, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 11, 29, 29, 43, 43, 1, 1, 19, 19] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50, 51]) total number of confs: 266 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114107 none CC(=O)N1CCCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 88, 109, 88, 88, 88, 88, 30, 30, 30, 11, 11, 11, 1, 1, 1, 1, 1, 5, 7, 8, 8, 8, 8, 1, 1, 11, 88, 109, 109, 109, 88, 88, 88, 88, 88, 88, 88, 30, 11, 11, 11, 11, 1, 5, 5, 7, 7, 11, 11, 88, 88] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 338 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114107 none CC(=O)N1CCCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 88, 88, 88, 150, 193, 196, 196, 196, 196, 88, 88, 19, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 19, 19, 19, 19, 88, 150, 150, 193, 193, 19, 19, 1, 1] 201 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 33, 8, 7, 50, 35, 36, 27, 51, 37, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 724 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114107 none CC(=O)N1CCCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 195, 201, 195, 195, 195, 195, 88, 88, 88, 46, 46, 46, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 46, 195, 201, 201, 201, 195, 195, 195, 195, 195, 195, 195, 88, 46, 46, 46, 46, 9, 5, 5, 3, 3, 46, 46, 195, 195] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 573 number of broken/clashed sets: 2 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114107 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114107/1 /scratch/stefan/7770410/working/building/REAL300020114107 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1832) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1832 `/scratch/stefan/7770410/working/3D/1832' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1) `REAL300020114107.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114107 none CC(=O)N1CCCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 19, 30, 19, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 30, 44, 48, 48, 48, 48, 11, 11, 1, 19, 30, 30, 30, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 11, 30, 30, 44, 44, 1, 1, 19, 19] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50, 51]) total number of confs: 271 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114107 none CC(=O)N1CCCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 87, 108, 87, 87, 87, 87, 30, 30, 30, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 87, 108, 108, 108, 87, 87, 87, 87, 87, 87, 87, 30, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 87, 87] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 341 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114107 none CC(=O)N1CCCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 87, 87, 87, 150, 193, 197, 197, 197, 197, 87, 87, 19, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 19, 19, 19, 19, 87, 150, 150, 193, 193, 19, 19, 1, 1] 201 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 33, 8, 7, 50, 35, 36, 27, 51, 37, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 725 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114107 none CC(=O)N1CCCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 197, 201, 197, 197, 197, 197, 90, 90, 90, 48, 48, 48, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 48, 197, 201, 201, 201, 197, 197, 197, 197, 197, 197, 197, 90, 48, 48, 48, 48, 10, 5, 5, 3, 3, 48, 48, 197, 197] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 568 number of broken/clashed sets: 2 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114107 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114107 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114107/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114107/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114107 Building REAL300020114108 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114108' /scratch/stefan/7770410/working/building/REAL300020114108 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114108 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114108/0 /scratch/stefan/7770410/working/building/REAL300020114108 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1833) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1833 `/scratch/stefan/7770410/working/3D/1833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2=CC=CC=C2O1) `REAL300020114108.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114108 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 53, 119, 119, 119, 119, 119, 119, 119, 119, 53, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 119, 119, 119, 119, 119, 119, 119] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 369 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114108 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [178, 178, 67, 67, 67, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 67, 178, 201, 201, 201, 201, 201, 201, 201, 201, 178, 67, 67, 67, 67, 11, 6, 6, 4, 4, 67, 67, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 563 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114108 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 39, 57, 66, 66, 66, 66, 13, 13, 1, 6, 25, 25, 25, 25, 25, 25, 25, 25, 6, 1, 1, 1, 1, 13, 39, 39, 57, 57, 1, 1, 25, 25, 25, 25, 25, 25, 25] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 308 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114108 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 25, 25, 25, 119, 119, 119, 178, 201, 201, 201, 201, 201, 119, 119, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 25, 25, 25, 25, 119, 178, 178, 201, 201, 25, 25, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 637 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114108 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114108/1 /scratch/stefan/7770410/working/building/REAL300020114108 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1834) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1834 `/scratch/stefan/7770410/working/3D/1834' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2=CC=CC=C2O1) `REAL300020114108.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114108 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 53, 120, 120, 120, 120, 120, 120, 120, 120, 53, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 120, 120, 120, 120, 120, 120, 120] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 373 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114108 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [178, 178, 66, 66, 66, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 66, 178, 201, 201, 201, 201, 201, 201, 201, 201, 178, 66, 66, 66, 66, 11, 6, 6, 4, 4, 66, 66, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 563 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114108 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 38, 56, 65, 65, 65, 65, 13, 13, 1, 6, 25, 25, 25, 25, 25, 25, 25, 25, 6, 1, 1, 1, 1, 13, 38, 38, 56, 56, 1, 1, 25, 25, 25, 25, 25, 25, 25] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 305 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114108 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 25, 25, 25, 120, 120, 120, 177, 201, 201, 201, 201, 201, 120, 120, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 25, 25, 25, 25, 120, 177, 177, 201, 201, 25, 25, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 629 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114108 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114108 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114108/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114108/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114108 Building REAL300020114109 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114109' /scratch/stefan/7770410/working/building/REAL300020114109 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114109 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114109/0 /scratch/stefan/7770410/working/building/REAL300020114109 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1835) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1835 `/scratch/stefan/7770410/working/3D/1835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(Cl)C=C1F) `REAL300020114109.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114109 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(Cl)C=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 16, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 12, 48, 101, 101, 52, 101, 101, 101, 101, 48, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 101, 101, 101] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 420 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114109 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(Cl)C=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 16, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 163, 95, 95, 95, 19, 19, 19, 6, 4, 1, 1, 1, 1, 1, 1, 19, 19, 95, 163, 201, 201, 168, 201, 201, 201, 201, 163, 95, 95, 95, 95, 19, 6, 6, 4, 4, 95, 95, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 675 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114109 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(Cl)C=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 16, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 56, 74, 90, 90, 90, 90, 12, 12, 1, 6, 20, 20, 8, 20, 20, 20, 20, 6, 1, 1, 1, 1, 12, 56, 56, 74, 74, 1, 1, 20, 20, 20] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 388 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114109 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(Cl)C=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 16, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 20, 20, 20, 101, 101, 101, 165, 201, 201, 201, 201, 201, 101, 101, 20, 1, 1, 1, 1, 1, 1, 1, 1, 8, 20, 20, 20, 20, 101, 165, 165, 201, 201, 20, 20, 1, 1, 1] 201 rigid atoms, others: [1, 39, 40, 41, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 712 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114109 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114109/1 /scratch/stefan/7770410/working/building/REAL300020114109 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1836) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1836 `/scratch/stefan/7770410/working/3D/1836' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(Cl)C=C1F) `REAL300020114109.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114109 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(Cl)C=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 16, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 12, 48, 103, 103, 52, 103, 103, 103, 103, 48, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 103, 103, 103] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 433 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114109 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(Cl)C=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 16, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 163, 90, 90, 90, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 90, 163, 201, 201, 169, 201, 201, 201, 201, 163, 90, 90, 90, 90, 18, 6, 6, 4, 4, 90, 90, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 678 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114109 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(Cl)C=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 16, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 57, 75, 93, 93, 93, 93, 12, 12, 1, 6, 22, 22, 8, 22, 22, 22, 22, 6, 1, 1, 1, 1, 12, 57, 57, 75, 75, 1, 1, 22, 22, 22] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 404 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114109 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(Cl)C=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 16, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 22, 22, 22, 103, 103, 103, 165, 201, 201, 201, 201, 201, 103, 103, 22, 1, 1, 1, 1, 1, 1, 1, 1, 8, 22, 22, 22, 22, 103, 165, 165, 201, 201, 22, 22, 1, 1, 1] 201 rigid atoms, others: [1, 39, 40, 41, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 712 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114109 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114109 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114109/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114109/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114109 Building REAL300020114110 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114110' /scratch/stefan/7770410/working/building/REAL300020114110 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114110 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114110/0 /scratch/stefan/7770410/working/building/REAL300020114110 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1837) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1837 `/scratch/stefan/7770410/working/3D/1837' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)N1CCCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1) `REAL300020114110.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114110 none NC(=O)N1CCCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 20, 34, 20, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 47, 50, 50, 50, 50, 11, 11, 1, 20, 34, 34, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 11, 31, 31, 47, 47, 1, 1, 20, 20] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50]) total number of confs: 296 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114110 none NC(=O)N1CCCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 92, 113, 92, 92, 92, 92, 35, 35, 35, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 92, 113, 113, 92, 92, 92, 92, 92, 92, 92, 35, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 92, 92] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 353 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114110 none NC(=O)N1CCCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 20, 20, 20, 92, 92, 92, 151, 193, 196, 196, 196, 196, 92, 92, 20, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 20, 20, 20, 20, 92, 151, 151, 193, 193, 20, 20, 1, 1] 201 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 33, 8, 7, 49, 50, 35, 36, 27, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 710 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114110 none NC(=O)N1CCCC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 196, 201, 196, 196, 196, 196, 101, 101, 101, 51, 51, 51, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 51, 196, 201, 201, 196, 196, 196, 196, 196, 196, 196, 101, 51, 51, 51, 51, 11, 6, 6, 4, 4, 51, 51, 196, 196] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 583 number of broken/clashed sets: 2 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114110 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114110/1 /scratch/stefan/7770410/working/building/REAL300020114110 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1838) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1838 `/scratch/stefan/7770410/working/3D/1838' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)N1CCCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1) `REAL300020114110.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114110 none NC(=O)N1CCCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 20, 33, 20, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 47, 51, 51, 51, 51, 11, 11, 1, 20, 33, 33, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 11, 31, 31, 47, 47, 1, 1, 20, 20] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50]) total number of confs: 296 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114110 none NC(=O)N1CCCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 92, 112, 92, 92, 92, 92, 35, 35, 35, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 92, 112, 112, 92, 92, 92, 92, 92, 92, 92, 35, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 92, 92] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 351 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114110 none NC(=O)N1CCCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 20, 20, 20, 92, 92, 92, 150, 192, 196, 196, 196, 196, 92, 92, 20, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 20, 20, 20, 20, 92, 150, 150, 192, 192, 20, 20, 1, 1] 201 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 33, 8, 7, 49, 50, 35, 36, 27, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 709 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114110 none NC(=O)N1CCCC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 197, 201, 197, 197, 197, 197, 99, 99, 99, 51, 51, 51, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 51, 197, 201, 201, 197, 197, 197, 197, 197, 197, 197, 99, 51, 51, 51, 51, 11, 6, 6, 4, 4, 51, 51, 197, 197] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 581 number of broken/clashed sets: 2 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114110 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114110 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114110/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114110/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114110 Building REAL300020114111 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114111' /scratch/stefan/7770410/working/building/REAL300020114111 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114111 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114111/0 /scratch/stefan/7770410/working/building/REAL300020114111 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1839) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1839 `/scratch/stefan/7770410/working/3D/1839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1F) `REAL300020114111.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114111 none CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 32, 45, 49, 49, 49, 49, 9, 9, 1, 16, 16, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 9, 32, 32, 45, 45, 1, 1, 16] 201 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 214 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114111 none CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 24, 24, 24, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 71, 71, 71, 71, 71, 71, 71, 71, 24, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 71] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 162 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114111 none CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 71, 71, 71, 146, 201, 201, 201, 201, 201, 71, 71, 16, 1, 1, 1, 2, 2, 2, 1, 1, 5, 16, 16, 16, 16, 71, 146, 146, 201, 201, 16, 16, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 836 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114111 none CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 77, 77, 77, 50, 50, 50, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 50, 201, 201, 201, 201, 201, 201, 201, 201, 77, 50, 50, 50, 50, 11, 6, 6, 4, 4, 50, 50, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 400 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114111 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114111/1 /scratch/stefan/7770410/working/building/REAL300020114111 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1840) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1840 `/scratch/stefan/7770410/working/3D/1840' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1F) `REAL300020114111.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114111 none CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 32, 45, 49, 49, 49, 49, 9, 9, 1, 16, 16, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 9, 32, 32, 45, 45, 1, 1, 16] 201 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 214 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114111 none CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 24, 24, 24, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 71, 71, 71, 71, 71, 71, 71, 71, 24, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 71] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 162 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114111 none CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 71, 71, 71, 146, 201, 201, 201, 201, 201, 71, 71, 16, 1, 1, 1, 2, 2, 2, 1, 1, 5, 16, 16, 16, 16, 71, 146, 146, 201, 201, 16, 16, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 836 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114111 none CC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 77, 77, 77, 50, 50, 50, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 50, 201, 201, 201, 201, 201, 201, 201, 201, 77, 50, 50, 50, 50, 11, 6, 6, 4, 4, 50, 50, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 400 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114111 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114111 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114111/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114111/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114111 Building REAL300020114112 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114112' /scratch/stefan/7770410/working/building/REAL300020114112 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114112 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114112/0 /scratch/stefan/7770410/working/building/REAL300020114112 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1841) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1841 `/scratch/stefan/7770410/working/3D/1841' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC=C1C) `REAL300020114112.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114112 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 14, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 29, 42, 42, 42, 42, 42, 10, 10, 1, 14, 14, 14, 14, 22, 22, 22, 14, 5, 1, 1, 1, 1, 10, 29, 29, 42, 42, 1, 1, 14, 14, 14, 14, 14] 201 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48]) total number of confs: 204 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114112 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 70, 70, 70, 24, 24, 24, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 10, 70, 70, 70, 70, 95, 95, 95, 70, 24, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 70, 70, 70, 70, 70] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 206 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114112 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 70, 70, 70, 145, 201, 201, 201, 201, 201, 70, 70, 14, 1, 1, 1, 1, 4, 4, 4, 1, 5, 14, 14, 14, 14, 70, 145, 145, 201, 201, 14, 14, 1, 1, 2, 2, 2] 201 rigid atoms, others: [1, 2, 3, 4, 5, 44, 45, 24, 25, 26, 27, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 825 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114112 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 76, 76, 76, 43, 43, 43, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 43, 201, 201, 201, 201, 201, 201, 201, 201, 76, 43, 43, 43, 43, 9, 4, 4, 2, 2, 43, 43, 201, 201, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 386 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114112 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114112/1 /scratch/stefan/7770410/working/building/REAL300020114112 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1842) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1842 `/scratch/stefan/7770410/working/3D/1842' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC=C1C) `REAL300020114112.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114112 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 14, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 30, 43, 44, 44, 44, 44, 10, 10, 1, 14, 14, 14, 14, 22, 22, 22, 14, 5, 1, 1, 1, 1, 10, 30, 30, 43, 43, 1, 1, 14, 14, 14, 14, 14] 201 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48]) total number of confs: 209 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114112 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 68, 68, 68, 24, 24, 24, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 10, 68, 68, 68, 68, 94, 94, 94, 68, 24, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 68, 68, 68, 68, 68] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 206 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114112 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 68, 68, 68, 144, 200, 201, 201, 201, 201, 68, 68, 14, 1, 1, 1, 1, 4, 4, 4, 1, 5, 14, 14, 14, 14, 68, 144, 144, 200, 200, 14, 14, 1, 1, 2, 2, 2] 201 rigid atoms, others: [1, 2, 3, 4, 5, 44, 45, 24, 25, 26, 27, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 827 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114112 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 76, 76, 76, 44, 44, 44, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 44, 201, 201, 201, 201, 201, 201, 201, 201, 76, 44, 44, 44, 44, 10, 5, 5, 3, 3, 44, 44, 201, 201, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 387 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114112 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114112 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114112/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114112/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114112 Building REAL300020114113 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114113' /scratch/stefan/7770410/working/building/REAL300020114113 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114113 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114113/0 /scratch/stefan/7770410/working/building/REAL300020114113 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1843) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1843 `/scratch/stefan/7770410/working/3D/1843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(Cl)=CC=C1F) `REAL300020114113.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114113 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 16, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 8, 12, 16, 16, 16, 16, 1, 1, 6, 20, 80, 80, 80, 35, 80, 80, 80, 20, 6, 6, 6, 6, 1, 8, 8, 12, 12, 6, 6, 80, 20, 80] 145 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 277 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114113 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 16, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 44, 44, 44, 20, 20, 20, 8, 4, 1, 1, 1, 1, 1, 1, 20, 20, 44, 74, 145, 145, 145, 124, 145, 145, 145, 74, 44, 44, 44, 44, 20, 8, 8, 4, 4, 44, 44, 145, 76, 145] 145 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 422 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114113 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 16, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 21, 32, 40, 40, 40, 40, 6, 6, 1, 6, 43, 43, 43, 9, 43, 43, 43, 6, 1, 1, 1, 1, 6, 21, 21, 32, 32, 1, 1, 43, 6, 43] 145 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114113 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC(Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 16, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 43, 43, 43, 80, 80, 80, 130, 145, 145, 145, 145, 145, 80, 80, 43, 1, 1, 1, 1, 1, 1, 1, 1, 12, 43, 43, 43, 43, 80, 130, 130, 145, 145, 43, 43, 1, 1, 1] 145 rigid atoms, others: [1, 39, 40, 41, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 515 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114113 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114113/1 /scratch/stefan/7770410/working/building/REAL300020114113 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1844) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1844 `/scratch/stefan/7770410/working/3D/1844' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(Cl)=CC=C1F) `REAL300020114113.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114113 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 16, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 8, 12, 16, 16, 16, 16, 1, 1, 6, 20, 79, 79, 79, 36, 79, 79, 79, 20, 6, 6, 6, 6, 1, 8, 8, 12, 12, 6, 6, 79, 20, 79] 144 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 277 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114113 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 16, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 44, 44, 44, 20, 20, 20, 8, 4, 1, 1, 1, 1, 1, 1, 20, 20, 44, 74, 144, 144, 144, 122, 144, 144, 144, 74, 44, 44, 44, 44, 20, 8, 8, 4, 4, 44, 44, 144, 75, 144] 144 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 422 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114113 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 16, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 21, 32, 40, 40, 40, 40, 6, 6, 1, 6, 43, 43, 43, 7, 43, 43, 43, 6, 1, 1, 1, 1, 6, 21, 21, 32, 32, 1, 1, 43, 6, 43] 144 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114113 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC(Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 16, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 43, 43, 43, 79, 79, 79, 129, 144, 144, 144, 144, 144, 79, 79, 43, 1, 1, 1, 1, 1, 1, 1, 1, 12, 43, 43, 43, 43, 79, 129, 129, 144, 144, 43, 43, 1, 1, 1] 144 rigid atoms, others: [1, 39, 40, 41, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 513 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114113 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114113 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114113/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114113/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114113 Building REAL300020114114 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114114' /scratch/stefan/7770410/working/building/REAL300020114114 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114114 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114114/0 /scratch/stefan/7770410/working/building/REAL300020114114 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1845) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1845 `/scratch/stefan/7770410/working/3D/1845' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1) `REAL300020114114.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114114 none CCCCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 5, 5, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 33, 45, 48, 48, 48, 48, 9, 9, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 9, 33, 33, 45, 45, 1, 1, 16, 16] 201 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 44, 50, 51, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 270 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114114 none CCCCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 23, 23, 73, 73, 23, 23, 23, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 23, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 73, 73] 201 rigid atoms, others: [45, 14, 13, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 459 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114114 none CCCCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 73, 73, 73, 152, 201, 201, 201, 201, 201, 73, 73, 16, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 73, 152, 152, 201, 201, 16, 16, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 32, 37, 6, 33, 8, 5, 34, 27, 35, 52, 53, 7, 4, 38, 28, 39, 36] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 805 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114114 none CCCCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 79, 79, 201, 201, 79, 79, 79, 48, 48, 48, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 48, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 79, 48, 48, 48, 48, 11, 6, 6, 4, 4, 48, 48, 201, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 1189 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114114 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114114/1 /scratch/stefan/7770410/working/building/REAL300020114114 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1846) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1846 `/scratch/stefan/7770410/working/3D/1846' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1) `REAL300020114114.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114114 none CCCCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 5, 5, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 33, 45, 48, 48, 48, 48, 9, 9, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 9, 33, 33, 45, 45, 1, 1, 16, 16] 201 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 44, 50, 51, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 270 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114114 none CCCCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 23, 23, 73, 73, 23, 23, 23, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 23, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 73, 73] 201 rigid atoms, others: [45, 14, 13, 16, 17, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 459 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114114 none CCCCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 73, 73, 73, 152, 201, 201, 201, 201, 201, 73, 73, 16, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 73, 152, 152, 201, 201, 16, 16, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 32, 37, 6, 33, 8, 5, 34, 27, 35, 52, 53, 7, 4, 38, 28, 39, 36] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 800 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114114 none CCCCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 79, 79, 201, 201, 79, 79, 79, 48, 48, 48, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 48, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 79, 48, 48, 48, 48, 11, 6, 6, 4, 4, 48, 48, 201, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 1195 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114114 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114114 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114114/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114114/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114114 Building REAL300020114115 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114115' /scratch/stefan/7770410/working/building/REAL300020114115 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114115 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114115/0 /scratch/stefan/7770410/working/building/REAL300020114115 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1847) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1847 `/scratch/stefan/7770410/working/3D/1847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C2=CC=CC=C2)CCC1) `REAL300020114115.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114115 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C2=CC=CC=C2)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 13, 58, 161, 161, 161, 161, 161, 161, 161, 161, 161, 58, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 161, 161, 161, 161, 161, 161, 161, 161, 161, 161, 161] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 454 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114115 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C2=CC=CC=C2)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 2, 9, 9, 29, 29, 29, 161, 161, 161, 187, 201, 201, 201, 201, 201, 161, 161, 29, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 29, 29, 29, 29, 161, 187, 187, 201, 201, 29, 29, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48, 49, 50, 51]) total number of confs: 464 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114115 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C2=CC=CC=C2)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 29, 29, 29, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 29, 87, 201, 201, 201, 201, 201, 201, 201, 201, 201, 87, 29, 29, 29, 29, 7, 4, 4, 2, 2, 29, 29, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 570 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114115 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C2=CC=CC=C2)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 21, 29, 29, 29, 29, 29, 13, 13, 1, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 13, 21, 21, 29, 29, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 172 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114115 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1(C2=CC=CC=C2)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 29, 29, 29, 161, 161, 161, 187, 201, 201, 201, 201, 201, 161, 161, 29, 1, 1, 2, 2, 1, 2, 2, 1, 1, 1, 9, 29, 29, 29, 29, 161, 187, 187, 201, 201, 29, 29, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 51, 46, 47, 48, 49, 50, 19, 20, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 467 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114115 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114115/1 /scratch/stefan/7770410/working/building/REAL300020114115 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1848) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1848 `/scratch/stefan/7770410/working/3D/1848' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C2=CC=CC=C2)CCC1) `REAL300020114115.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114115/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114115 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C2=CC=CC=C2)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 13, 58, 161, 161, 161, 161, 161, 161, 161, 161, 161, 58, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 161, 161, 161, 161, 161, 161, 161, 161, 161, 161, 161] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 454 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114115 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C2=CC=CC=C2)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 2, 9, 9, 29, 29, 29, 161, 161, 161, 187, 201, 201, 201, 201, 201, 161, 161, 29, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 29, 29, 29, 29, 161, 187, 187, 201, 201, 29, 29, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48, 49, 50, 51]) total number of confs: 464 number of broken/clashed sets: 1 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114115 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C2=CC=CC=C2)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 29, 29, 29, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 29, 87, 201, 201, 201, 201, 201, 201, 201, 201, 201, 87, 29, 29, 29, 29, 7, 4, 4, 2, 2, 29, 29, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 570 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114115 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C2=CC=CC=C2)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 21, 29, 29, 29, 29, 29, 13, 13, 1, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 13, 21, 21, 29, 29, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 172 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114115 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1(C2=CC=CC=C2)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 29, 29, 29, 161, 161, 161, 187, 201, 201, 201, 201, 201, 161, 161, 29, 1, 1, 2, 2, 1, 2, 2, 1, 1, 1, 9, 29, 29, 29, 29, 161, 187, 187, 201, 201, 29, 29, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 51, 46, 47, 48, 49, 50, 19, 20, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 467 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114115 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114115 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114115/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114115/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114115 Building REAL300020114116 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114116' /scratch/stefan/7770410/working/building/REAL300020114116 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114116 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114116/0 /scratch/stefan/7770410/working/building/REAL300020114116 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1849) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1849 `/scratch/stefan/7770410/working/3D/1849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1COC2=CC=CC=C2C1) `REAL300020114116.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114116 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1COC2=CC=CC=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 33, 105, 105, 105, 105, 105, 105, 105, 105, 105, 33, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 105, 105, 105, 105, 105, 105, 105, 105, 105] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 302 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114116 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1COC2=CC=CC=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 56, 56, 56, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 56, 108, 201, 201, 201, 201, 201, 201, 201, 201, 201, 108, 56, 56, 56, 56, 12, 6, 6, 4, 4, 56, 56, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 600 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114116 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1COC2=CC=CC=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 31, 46, 55, 55, 55, 55, 11, 11, 1, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 11, 31, 31, 46, 46, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114116 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1COC2=CC=CC=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 23, 23, 23, 105, 105, 105, 178, 201, 201, 201, 201, 201, 105, 105, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 23, 23, 23, 23, 105, 178, 178, 201, 201, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 695 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114116 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114116/1 /scratch/stefan/7770410/working/building/REAL300020114116 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1850) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1850 `/scratch/stefan/7770410/working/3D/1850' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1COC2=CC=CC=C2C1) `REAL300020114116.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114116/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114116 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1COC2=CC=CC=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 33, 107, 107, 107, 107, 107, 107, 107, 107, 107, 33, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 107, 107, 107, 107, 107, 107, 107, 107, 107] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 308 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114116 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1COC2=CC=CC=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 57, 57, 57, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 57, 108, 201, 201, 201, 201, 201, 201, 201, 201, 201, 108, 57, 57, 57, 57, 13, 6, 6, 4, 4, 57, 57, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 601 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114116 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1COC2=CC=CC=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 30, 45, 54, 54, 54, 54, 11, 11, 1, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 11, 30, 30, 45, 45, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 259 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114116 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1COC2=CC=CC=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 24, 24, 24, 107, 107, 107, 178, 201, 201, 201, 201, 201, 107, 107, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 24, 24, 24, 24, 107, 178, 178, 201, 201, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 686 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114116 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114116 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114116/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114116/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114116 Building REAL300020114117 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114117' /scratch/stefan/7770410/working/building/REAL300020114117 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114117 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114117/0 /scratch/stefan/7770410/working/building/REAL300020114117 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1851) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1851 `/scratch/stefan/7770410/working/3D/1851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C2=CC=CC=C2N1) `REAL300020114117.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114117 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C2=CC=CC=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 28, 41, 43, 43, 43, 43, 8, 8, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 8, 28, 28, 41, 41, 1, 1, 19, 19, 19, 19, 19] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 42, 43, 21] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48]) total number of confs: 200 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114117 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C2=CC=CC=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 23, 23, 23, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 23, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 88, 88, 88, 88, 88] 201 rigid atoms, others: [37, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 176 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114117 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C2=CC=CC=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 19, 19, 19, 88, 88, 88, 162, 201, 201, 201, 201, 201, 88, 88, 19, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 19, 19, 19, 19, 88, 162, 162, 201, 201, 19, 19, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 45, 46, 47, 48, 22, 23, 24, 25, 26, 27, 28] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 774 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114117 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C2=CC=CC=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 85, 85, 85, 43, 43, 43, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 43, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 85, 43, 43, 43, 43, 9, 5, 5, 3, 3, 43, 43, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 409 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114117 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114117/1 /scratch/stefan/7770410/working/building/REAL300020114117 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1852) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1852 `/scratch/stefan/7770410/working/3D/1852' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C2=CC=CC=C2N1) `REAL300020114117.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114117 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C2=CC=CC=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 27, 40, 42, 42, 42, 42, 8, 8, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 8, 27, 27, 40, 40, 1, 1, 19, 19, 19, 19, 19] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 42, 43, 21] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48]) total number of confs: 197 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114117 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C2=CC=CC=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 23, 23, 23, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 8, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 23, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 88, 88, 88, 88, 88] 201 rigid atoms, others: [37, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 176 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114117 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C2=CC=CC=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 19, 19, 19, 88, 88, 88, 162, 201, 201, 201, 201, 201, 88, 88, 19, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 19, 19, 19, 19, 88, 162, 162, 201, 201, 19, 19, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 45, 46, 47, 48, 22, 23, 24, 25, 26, 27, 28] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 774 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114117 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C2=CC=CC=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 85, 85, 85, 43, 43, 43, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 43, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 85, 43, 43, 43, 43, 9, 5, 5, 3, 3, 43, 43, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 409 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114117 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114117 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114117/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114117/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114117 Building REAL300020114118 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114118' /scratch/stefan/7770410/working/building/REAL300020114118 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114118 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114118/0 /scratch/stefan/7770410/working/building/REAL300020114118 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1853) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1853 `/scratch/stefan/7770410/working/3D/1853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C(C)O1) `REAL300020114118.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114118 none CC1=C(C)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 26, 39, 39, 39, 39, 39, 11, 11, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 11, 26, 26, 39, 39, 1, 1, 21, 21, 21] 201 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 187 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114118 none CC1=C(C)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 86, 28, 28, 28, 11, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 11, 86, 86, 86, 86, 86, 86, 86, 86, 86, 28, 11, 11, 11, 11, 1, 5, 5, 7, 7, 11, 11, 86, 86, 86] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 176 number of broken/clashed sets: 20 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114118 none CC1=C(C)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 21, 21, 21, 86, 86, 86, 152, 201, 201, 201, 201, 201, 86, 86, 21, 1, 1, 1, 2, 2, 2, 2, 2, 2, 8, 21, 21, 21, 21, 86, 152, 152, 201, 201, 21, 21, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 799 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114118 none CC1=C(C)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 72, 72, 72, 40, 40, 40, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 40, 201, 201, 201, 201, 201, 201, 201, 201, 201, 72, 40, 40, 40, 40, 8, 4, 4, 2, 2, 40, 40, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 388 number of broken/clashed sets: 20 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114118 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114118/1 /scratch/stefan/7770410/working/building/REAL300020114118 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1854) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1854 `/scratch/stefan/7770410/working/3D/1854' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C(C)O1) `REAL300020114118.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114118 none CC1=C(C)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 26, 39, 39, 39, 39, 39, 11, 11, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 11, 26, 26, 39, 39, 1, 1, 21, 21, 21] 201 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 187 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114118 none CC1=C(C)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 86, 28, 28, 28, 11, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 11, 86, 86, 86, 86, 86, 86, 86, 86, 86, 28, 11, 11, 11, 11, 1, 5, 5, 7, 7, 11, 11, 86, 86, 86] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 176 number of broken/clashed sets: 20 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114118 none CC1=C(C)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 21, 21, 21, 86, 86, 86, 152, 201, 201, 201, 201, 201, 86, 86, 21, 1, 1, 1, 2, 2, 2, 2, 2, 2, 8, 21, 21, 21, 21, 86, 152, 152, 201, 201, 21, 21, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 799 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114118 none CC1=C(C)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 71, 71, 71, 40, 40, 40, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 40, 201, 201, 201, 201, 201, 201, 201, 201, 201, 71, 40, 40, 40, 40, 8, 4, 4, 2, 2, 40, 40, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 386 number of broken/clashed sets: 20 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114118 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114118 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114118/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114118/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114118 Building REAL300020114119 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114119' /scratch/stefan/7770410/working/building/REAL300020114119 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114119 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114119/0 /scratch/stefan/7770410/working/building/REAL300020114119 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1855) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1855 `/scratch/stefan/7770410/working/3D/1855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1) `REAL300020114119.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114119 none COC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 42, 58, 63, 63, 63, 63, 11, 11, 1, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 11, 42, 42, 58, 58, 1, 1, 16] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 261 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114119 none COC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 91, 91, 35, 35, 35, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 91, 91, 91, 91, 91, 91, 91, 35, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 91] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 213 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114119 none COC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 91, 91, 91, 165, 201, 201, 201, 201, 201, 91, 91, 16, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 91, 165, 165, 201, 201, 16, 16, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 44, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 724 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114119 none COC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 134, 134, 134, 65, 65, 65, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 65, 201, 201, 201, 201, 201, 201, 201, 134, 65, 65, 65, 65, 14, 6, 6, 4, 4, 65, 65, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 514 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114119 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114119/1 /scratch/stefan/7770410/working/building/REAL300020114119 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1856) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1856 `/scratch/stefan/7770410/working/3D/1856' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1) `REAL300020114119.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114119/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114119 none COC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 41, 57, 63, 63, 63, 63, 11, 11, 1, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 11, 41, 41, 57, 57, 1, 1, 16] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 260 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114119 none COC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 90, 90, 35, 35, 35, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 13, 13, 13, 13, 1, 1, 11, 90, 90, 90, 90, 90, 90, 90, 35, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 90] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 214 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114119 none COC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 90, 90, 90, 165, 201, 201, 201, 201, 201, 90, 90, 16, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 90, 165, 165, 201, 201, 16, 16, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 44, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 729 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114119 none COC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 133, 133, 133, 63, 63, 63, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 63, 201, 201, 201, 201, 201, 201, 201, 133, 63, 63, 63, 63, 12, 6, 6, 4, 4, 63, 63, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 518 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114119 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114119 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114119/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114119/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114119 Building REAL300020114120 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114120' /scratch/stefan/7770410/working/building/REAL300020114120 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114120 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114120/0 /scratch/stefan/7770410/working/building/REAL300020114120 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1857) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1857 `/scratch/stefan/7770410/working/3D/1857' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=C1) `REAL300020114120.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114120 none CC1=NN(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 38, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 18, 26, 26, 26, 26, 26, 6, 6, 1, 67, 67, 67, 67, 67, 67, 38, 38, 6, 1, 1, 1, 1, 6, 18, 18, 26, 26, 1, 1, 67, 67, 67, 67] 136 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 272 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114120 none CC1=NN(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 72, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 7, 9, 9, 9, 9, 9, 1, 1, 6, 101, 101, 101, 101, 101, 101, 72, 72, 20, 6, 6, 6, 6, 1, 7, 7, 9, 9, 6, 6, 101, 101, 101, 101] 136 rigid atoms, others: [37, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 337 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114120 none CC1=NN(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 37, 36, 37, 67, 67, 67, 101, 101, 101, 129, 136, 136, 136, 136, 136, 101, 101, 67, 1, 1, 1, 2, 2, 2, 6, 6, 36, 67, 67, 67, 67, 101, 129, 129, 136, 136, 67, 67, 2, 2, 2, 1] 136 rigid atoms, others: [0, 1, 2, 3, 4, 47, 24, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 456 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114120 none CC1=NN(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 133, 114, 56, 56, 56, 31, 31, 31, 13, 13, 13, 6, 2, 1, 1, 1, 1, 1, 1, 13, 13, 31, 133, 133, 133, 133, 133, 133, 114, 114, 56, 31, 31, 31, 31, 13, 6, 6, 2, 2, 31, 31, 133, 133, 133, 133] 133 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 469 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114120 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114120/1 /scratch/stefan/7770410/working/building/REAL300020114120 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1858) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1858 `/scratch/stefan/7770410/working/3D/1858' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=C1) `REAL300020114120.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114120/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114120 none CC1=NN(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 38, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 18, 25, 25, 25, 25, 25, 6, 6, 1, 67, 67, 67, 67, 67, 67, 38, 38, 6, 1, 1, 1, 1, 6, 18, 18, 25, 25, 1, 1, 67, 67, 67, 67] 134 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 266 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114120 none CC1=NN(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 71, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 7, 9, 9, 9, 9, 9, 1, 1, 6, 100, 100, 100, 100, 100, 100, 71, 71, 19, 6, 6, 6, 6, 1, 7, 7, 9, 9, 6, 6, 100, 100, 100, 100] 134 rigid atoms, others: [37, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 333 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114120 none CC1=NN(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 37, 36, 37, 67, 67, 67, 100, 100, 100, 128, 134, 134, 134, 134, 134, 100, 100, 67, 1, 1, 1, 2, 2, 2, 6, 6, 36, 67, 67, 67, 67, 100, 128, 128, 134, 134, 67, 67, 2, 2, 2, 1] 134 rigid atoms, others: [0, 1, 2, 3, 4, 47, 24, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 448 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114120 none CC1=NN(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 131, 112, 55, 55, 55, 30, 30, 30, 13, 13, 13, 6, 2, 1, 1, 1, 1, 1, 1, 13, 13, 30, 131, 131, 131, 131, 131, 131, 112, 112, 55, 30, 30, 30, 30, 13, 6, 6, 2, 2, 30, 30, 131, 131, 131, 131] 131 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 459 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114120 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114120 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114120/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114120/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114120 Building REAL300020114121 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114121' /scratch/stefan/7770410/working/building/REAL300020114121 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114121 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114121/0 /scratch/stefan/7770410/working/building/REAL300020114121 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1859) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1859 `/scratch/stefan/7770410/working/3D/1859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1) `REAL300020114121.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114121 none COCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 23, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 27, 40, 43, 43, 43, 43, 8, 8, 1, 6, 28, 28, 28, 23, 23, 6, 6, 6, 1, 1, 1, 1, 8, 27, 27, 40, 40, 1, 1] 201 rigid atoms, others: [45, 35, 36, 37, 38, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 259 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114121 none COCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 84, 29, 29, 29, 29, 29, 29, 29, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 8, 29, 99, 99, 99, 84, 84, 29, 29, 29, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 365 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114121 none COCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 29, 29, 29, 68, 91, 94, 94, 94, 94, 29, 29, 6, 1, 13, 13, 13, 9, 9, 1, 1, 1, 6, 6, 6, 6, 29, 68, 68, 91, 91, 6, 6] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 26] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 400 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114121 none COCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 95, 95, 95, 95, 95, 95, 95, 42, 42, 42, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 42, 95, 201, 201, 201, 201, 201, 95, 95, 95, 42, 42, 42, 42, 11, 6, 6, 4, 4, 42, 42] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 767 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114121 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114121/1 /scratch/stefan/7770410/working/building/REAL300020114121 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1860) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1860 `/scratch/stefan/7770410/working/3D/1860' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1) `REAL300020114121.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114121/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114121 none COCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 23, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 27, 40, 43, 43, 43, 43, 8, 8, 1, 6, 28, 28, 28, 23, 23, 6, 6, 6, 1, 1, 1, 1, 8, 27, 27, 40, 40, 1, 1] 201 rigid atoms, others: [45, 35, 36, 37, 38, 9, 10, 11, 12, 13, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 259 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114121 none COCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 84, 29, 29, 29, 29, 29, 29, 29, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 8, 29, 99, 99, 99, 84, 84, 29, 29, 29, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 365 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114121 none COCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 29, 29, 29, 68, 91, 94, 94, 94, 94, 29, 29, 6, 1, 13, 13, 13, 9, 9, 1, 1, 1, 6, 6, 6, 6, 29, 68, 68, 91, 91, 6, 6] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 26] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 400 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114121 none COCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 95, 95, 95, 95, 95, 95, 95, 41, 41, 41, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 41, 95, 201, 201, 201, 201, 201, 95, 95, 95, 41, 41, 41, 41, 10, 6, 6, 4, 4, 41, 41] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 772 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114121 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114121 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114121/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114121/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114121 Building REAL300020114122 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114122' /scratch/stefan/7770410/working/building/REAL300020114122 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114122 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114122/0 /scratch/stefan/7770410/working/building/REAL300020114122 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1861) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1861 `/scratch/stefan/7770410/working/3D/1861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(=O)OC(C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114122.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114122 none CC1=CC(=O)OC(C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 12, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 37, 53, 61, 61, 61, 61, 12, 12, 1, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 12, 37, 37, 53, 53, 1, 1] 201 rigid atoms, others: [45, 36, 37, 38, 39, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 257 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114122 none CC1=CC(=O)OC(C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 12, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 82, 82, 82, 82, 82, 41, 41, 41, 12, 12, 12, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 12, 82, 82, 82, 82, 82, 82, 82, 41, 12, 12, 12, 12, 1, 7, 7, 9, 9, 12, 12] 201 rigid atoms, others: [40, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 217 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114122 none CC1=CC(=O)OC(C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 12, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 82, 82, 82, 149, 201, 201, 201, 201, 201, 82, 82, 16, 2, 2, 2, 1, 2, 2, 2, 6, 16, 16, 16, 16, 82, 149, 149, 201, 201, 16, 16] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 786 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114122 none CC1=CC(=O)OC(C)=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 12, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 109, 109, 109, 61, 61, 61, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 61, 201, 201, 201, 201, 201, 201, 201, 109, 61, 61, 61, 61, 12, 6, 6, 4, 4, 61, 61] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 486 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114122 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114122/1 /scratch/stefan/7770410/working/building/REAL300020114122 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1862) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1862 `/scratch/stefan/7770410/working/3D/1862' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(=O)OC(C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114122.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114122/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114122 none CC1=CC(=O)OC(C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 12, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 33, 49, 57, 57, 57, 57, 12, 12, 1, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 12, 33, 33, 49, 49, 1, 1] 201 rigid atoms, others: [45, 36, 37, 38, 39, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 243 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114122 none CC1=CC(=O)OC(C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 12, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 83, 83, 83, 83, 83, 40, 40, 40, 12, 12, 12, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 12, 83, 83, 83, 83, 83, 83, 83, 40, 12, 12, 12, 12, 1, 6, 6, 8, 8, 12, 12] 201 rigid atoms, others: [40, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 213 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114122 none CC1=CC(=O)OC(C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 12, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 83, 83, 83, 148, 201, 201, 201, 201, 201, 83, 83, 17, 2, 2, 2, 1, 2, 2, 2, 6, 17, 17, 17, 17, 83, 148, 148, 201, 201, 17, 17] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 793 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114122 none CC1=CC(=O)OC(C)=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 12, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 109, 109, 109, 61, 61, 61, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 61, 201, 201, 201, 201, 201, 201, 201, 109, 61, 61, 61, 61, 12, 6, 6, 4, 4, 61, 61] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 486 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114122 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114122 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114122/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114122/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114122 Building REAL300020114123 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114123' /scratch/stefan/7770410/working/building/REAL300020114123 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114123 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114123/0 /scratch/stefan/7770410/working/building/REAL300020114123 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1863) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1863 `/scratch/stefan/7770410/working/3D/1863' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(Cl)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114123.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114123 none CN1C=C(Cl)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 55, 73, 91, 91, 91, 91, 12, 12, 1, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 12, 55, 55, 73, 73, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40]) total number of confs: 350 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114123 none CN1C=C(Cl)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 105, 105, 105, 51, 51, 51, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 12, 105, 105, 105, 105, 105, 51, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12] 201 rigid atoms, others: [36, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 256 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114123 none CN1C=C(Cl)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 20, 20, 20, 105, 105, 105, 166, 201, 201, 201, 201, 201, 105, 105, 20, 2, 2, 2, 1, 1, 8, 20, 20, 20, 20, 105, 166, 166, 201, 201, 20, 20] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 684 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114123 none CN1C=C(Cl)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 173, 173, 173, 92, 92, 92, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 92, 201, 201, 201, 201, 201, 173, 92, 92, 92, 92, 17, 6, 6, 4, 4, 92, 92] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 536 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114123 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114123/1 /scratch/stefan/7770410/working/building/REAL300020114123 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1864) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1864 `/scratch/stefan/7770410/working/3D/1864' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(Cl)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114123.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114123/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114123 none CN1C=C(Cl)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 55, 73, 91, 91, 91, 91, 12, 12, 1, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 12, 55, 55, 73, 73, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40]) total number of confs: 350 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114123 none CN1C=C(Cl)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 105, 105, 105, 51, 51, 51, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 12, 105, 105, 105, 105, 105, 51, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12] 201 rigid atoms, others: [36, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 256 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114123 none CN1C=C(Cl)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 20, 20, 20, 105, 105, 105, 166, 201, 201, 201, 201, 201, 105, 105, 20, 2, 2, 2, 1, 1, 8, 20, 20, 20, 20, 105, 166, 166, 201, 201, 20, 20] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 684 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114123 none CN1C=C(Cl)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 173, 173, 173, 92, 92, 92, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 92, 201, 201, 201, 201, 201, 173, 92, 92, 92, 92, 17, 6, 6, 4, 4, 92, 92] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 536 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114123 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114123 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114123/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114123/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114123 Building REAL300020114124 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114124' /scratch/stefan/7770410/working/building/REAL300020114124 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114124 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114124/0 /scratch/stefan/7770410/working/building/REAL300020114124 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1865) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1865 `/scratch/stefan/7770410/working/3D/1865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC1C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1(C)C) `REAL300020114124.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114124 none CC(C)=CC1C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 31, 40, 40, 40, 40, 40, 13, 13, 1, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 11, 11, 6, 1, 1, 1, 1, 13, 31, 31, 40, 40, 1, 1, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 47, 48, 40, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50, 51, 52, 53, 54]) total number of confs: 220 number of broken/clashed sets: 77 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114124 none CC(C)=CC1C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [129, 129, 129, 99, 99, 58, 58, 58, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 99, 99, 99, 129, 129, 129, 129, 129, 129, 129, 99, 99, 58, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 99, 99, 99, 99, 99, 99] 201 rigid atoms, others: [42, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 455 number of broken/clashed sets: 77 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114124 none CC(C)=CC1C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 99, 99, 99, 143, 170, 170, 170, 170, 170, 99, 99, 11, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 1, 1, 3, 11, 11, 11, 11, 99, 143, 143, 170, 170, 11, 11, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [3, 4, 5, 6, 35, 25, 26, 27, 36] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 544 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114124 none CC(C)=CC1C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 170, 170, 109, 109, 109, 40, 40, 40, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 40, 170, 170, 170, 201, 201, 201, 201, 201, 201, 201, 170, 170, 109, 40, 40, 40, 40, 8, 4, 4, 2, 2, 40, 40, 170, 170, 170, 170, 170, 170] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 667 number of broken/clashed sets: 77 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114124 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114124/1 /scratch/stefan/7770410/working/building/REAL300020114124 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1866) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1866 `/scratch/stefan/7770410/working/3D/1866' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC1C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1(C)C) `REAL300020114124.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114124 none CC(C)=CC1C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 31, 40, 40, 40, 40, 40, 13, 13, 1, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 11, 11, 6, 1, 1, 1, 1, 13, 31, 31, 40, 40, 1, 1, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 47, 48, 40, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50, 51, 52, 53, 54]) total number of confs: 220 number of broken/clashed sets: 77 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114124 none CC(C)=CC1C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [129, 129, 129, 99, 99, 58, 58, 58, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 13, 99, 99, 99, 129, 129, 129, 129, 129, 129, 129, 99, 99, 58, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 99, 99, 99, 99, 99, 99] 201 rigid atoms, others: [42, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 455 number of broken/clashed sets: 77 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114124 none CC(C)=CC1C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 99, 99, 99, 143, 170, 170, 170, 170, 170, 99, 99, 11, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 1, 1, 3, 11, 11, 11, 11, 99, 143, 143, 170, 170, 11, 11, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [3, 4, 5, 6, 35, 25, 26, 27, 36] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 544 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114124 none CC(C)=CC1C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 170, 170, 109, 109, 109, 40, 40, 40, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 40, 170, 170, 170, 201, 201, 201, 201, 201, 201, 201, 170, 170, 109, 40, 40, 40, 40, 8, 4, 4, 2, 2, 40, 40, 170, 170, 170, 170, 170, 170] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 667 number of broken/clashed sets: 77 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114124 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114124 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114124/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114124/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114124 Building REAL300020114125 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114125' /scratch/stefan/7770410/working/building/REAL300020114125 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114125 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114125/0 /scratch/stefan/7770410/working/building/REAL300020114125 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1867) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1867 `/scratch/stefan/7770410/working/3D/1867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC=C1C) `REAL300020114125.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114125 none COC1=CC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 27, 27, 27, 13, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 19, 30, 30, 30, 30, 30, 7, 7, 1, 27, 27, 27, 27, 41, 41, 41, 27, 13, 13, 5, 1, 1, 1, 1, 7, 19, 19, 30, 30, 1, 1, 27, 27, 27, 27, 27] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 45, 46, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51]) total number of confs: 225 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114125 none COC1=CC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [132, 117, 117, 117, 58, 21, 21, 21, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 117, 117, 117, 117, 132, 132, 132, 117, 58, 58, 21, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 117, 117, 117, 117, 117] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 374 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114125 none COC1=CC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 4, 11, 11, 11, 27, 27, 27, 117, 117, 117, 161, 201, 201, 201, 201, 201, 117, 117, 27, 1, 1, 1, 1, 3, 3, 3, 1, 4, 4, 11, 27, 27, 27, 27, 117, 161, 161, 201, 201, 27, 27, 1, 1, 2, 2, 2] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 47, 48, 25, 26, 27, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51]) total number of confs: 671 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114125 none COC1=CC(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 113, 51, 51, 51, 30, 30, 30, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 30, 201, 201, 201, 201, 201, 201, 201, 201, 113, 113, 51, 30, 30, 30, 30, 7, 4, 4, 2, 2, 30, 30, 201, 201, 201, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 596 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114125 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114125/1 /scratch/stefan/7770410/working/building/REAL300020114125 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1868) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1868 `/scratch/stefan/7770410/working/3D/1868' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC=C1C) `REAL300020114125.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114125 none COC1=CC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 27, 27, 27, 13, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 19, 30, 30, 30, 30, 30, 7, 7, 1, 27, 27, 27, 27, 41, 41, 41, 27, 13, 13, 5, 1, 1, 1, 1, 7, 19, 19, 30, 30, 1, 1, 27, 27, 27, 27, 27] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 45, 46, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51]) total number of confs: 225 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114125 none COC1=CC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [132, 117, 117, 117, 58, 21, 21, 21, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 117, 117, 117, 117, 132, 132, 132, 117, 58, 58, 21, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 117, 117, 117, 117, 117] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 375 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114125 none COC1=CC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 4, 11, 11, 11, 27, 27, 27, 117, 117, 117, 161, 201, 201, 201, 201, 201, 117, 117, 27, 1, 1, 1, 1, 3, 3, 3, 1, 4, 4, 11, 27, 27, 27, 27, 117, 161, 161, 201, 201, 27, 27, 1, 1, 2, 2, 2] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 47, 48, 25, 26, 27, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51]) total number of confs: 671 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114125 none COC1=CC(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 113, 51, 51, 51, 30, 30, 30, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 30, 201, 201, 201, 201, 201, 201, 201, 201, 113, 113, 51, 30, 30, 30, 30, 7, 4, 4, 2, 2, 30, 30, 201, 201, 201, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 597 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114125 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114125 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114125/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114125/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114125 Building REAL300020114126 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114126' /scratch/stefan/7770410/working/building/REAL300020114126 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114126 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114126/0 /scratch/stefan/7770410/working/building/REAL300020114126 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1869) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1869 `/scratch/stefan/7770410/working/3D/1869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1) `REAL300020114126.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114126 none CC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 31, 31, 23, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 22, 35, 35, 35, 35, 35, 8, 8, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 23, 23, 5, 1, 1, 1, 1, 8, 22, 22, 35, 35, 1, 1, 31, 31] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50]) total number of confs: 271 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114126 none CC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 114, 114, 91, 22, 22, 22, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 114, 114, 114, 114, 114, 114, 114, 114, 114, 91, 91, 22, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 114, 114] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 476 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114126 none CC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 4, 14, 14, 14, 31, 31, 31, 113, 113, 113, 167, 201, 201, 201, 201, 201, 113, 113, 31, 1, 1, 2, 2, 2, 1, 1, 3, 3, 4, 4, 14, 31, 31, 31, 31, 113, 167, 167, 201, 201, 31, 31, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 49, 50, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 713 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114126 none CC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 174, 62, 62, 62, 35, 35, 35, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 35, 201, 201, 201, 201, 201, 201, 201, 201, 201, 174, 174, 62, 35, 35, 35, 35, 8, 4, 4, 2, 2, 35, 35, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 803 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114126 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114126/1 /scratch/stefan/7770410/working/building/REAL300020114126 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1870) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1870 `/scratch/stefan/7770410/working/3D/1870' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1) `REAL300020114126.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114126/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114126 none CC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 31, 31, 23, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 22, 35, 35, 35, 35, 35, 8, 8, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 23, 23, 5, 1, 1, 1, 1, 8, 22, 22, 35, 35, 1, 1, 31, 31] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 47, 48, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50]) total number of confs: 271 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114126 none CC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 113, 113, 90, 22, 22, 22, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 113, 113, 113, 113, 113, 113, 113, 113, 113, 90, 90, 22, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 113, 113] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 473 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114126 none CC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 4, 14, 14, 14, 31, 31, 31, 113, 113, 113, 167, 201, 201, 201, 201, 201, 113, 113, 31, 1, 1, 2, 2, 2, 1, 1, 3, 3, 4, 4, 14, 31, 31, 31, 31, 113, 167, 167, 201, 201, 31, 31, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 49, 50, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 713 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114126 none CC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 174, 63, 63, 63, 35, 35, 35, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 35, 201, 201, 201, 201, 201, 201, 201, 201, 201, 174, 174, 63, 35, 35, 35, 35, 8, 4, 4, 2, 2, 35, 35, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 802 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114126 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114126 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114126/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114126/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114126 Building REAL300020114127 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114127' /scratch/stefan/7770410/working/building/REAL300020114127 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114127 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114127/0 /scratch/stefan/7770410/working/building/REAL300020114127 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1871) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1871 `/scratch/stefan/7770410/working/3D/1871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020114127.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114127 none COC1=CC=CC(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 47, 47, 47, 47, 47, 26, 22, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 16, 26, 26, 26, 26, 26, 7, 7, 1, 47, 62, 62, 62, 47, 47, 47, 26, 26, 22, 22, 5, 1, 1, 1, 1, 7, 16, 16, 26, 26, 1, 1, 47] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 51]) total number of confs: 279 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114127 none COC1=CC=CC(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [154, 148, 148, 148, 148, 148, 92, 77, 18, 18, 18, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 148, 154, 154, 154, 148, 148, 148, 92, 92, 77, 77, 18, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 148] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 503 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114127 none COC1=CC=CC(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 2, 6, 26, 26, 26, 47, 47, 47, 148, 148, 148, 173, 201, 201, 201, 201, 201, 148, 148, 47, 1, 3, 3, 3, 1, 1, 1, 2, 2, 6, 6, 26, 47, 47, 47, 47, 148, 173, 173, 201, 201, 47, 47, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 51, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 619 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114127 none COC1=CC=CC(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 145, 131, 41, 41, 41, 27, 27, 27, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 27, 201, 201, 201, 201, 201, 201, 201, 145, 145, 131, 131, 41, 27, 27, 27, 27, 7, 4, 4, 2, 2, 27, 27, 201] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 671 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114127 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114127/1 /scratch/stefan/7770410/working/building/REAL300020114127 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1872) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1872 `/scratch/stefan/7770410/working/3D/1872' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020114127.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114127 none COC1=CC=CC(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 49, 49, 49, 49, 49, 26, 22, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 16, 26, 26, 26, 26, 26, 7, 7, 1, 49, 63, 63, 63, 49, 49, 49, 26, 26, 22, 22, 5, 1, 1, 1, 1, 7, 16, 16, 26, 26, 1, 1, 49] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 51]) total number of confs: 281 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114127 none COC1=CC=CC(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [153, 149, 149, 149, 149, 149, 93, 77, 18, 18, 18, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 149, 153, 153, 153, 149, 149, 149, 93, 93, 77, 77, 18, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 149] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 505 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114127 none COC1=CC=CC(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 2, 6, 26, 26, 26, 49, 49, 49, 149, 149, 149, 172, 201, 201, 201, 201, 201, 149, 149, 49, 1, 3, 3, 3, 1, 1, 1, 2, 2, 6, 6, 26, 49, 49, 49, 49, 149, 172, 172, 201, 201, 49, 49, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 51, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 620 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114127 none COC1=CC=CC(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 145, 131, 41, 41, 41, 27, 27, 27, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 27, 201, 201, 201, 201, 201, 201, 201, 145, 145, 131, 131, 41, 27, 27, 27, 27, 7, 4, 4, 2, 2, 27, 27, 201] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 674 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114127 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114127 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114127/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114127/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114127 Building REAL300020114128 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114128' /scratch/stefan/7770410/working/building/REAL300020114128 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114128 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114128/0 /scratch/stefan/7770410/working/building/REAL300020114128 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1873) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1873 `/scratch/stefan/7770410/working/3D/1873' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC2=CNN=C2C=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114128.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114128 none O=C(CC1=CC2=CNN=C2C=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 12, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 7, 7, 7, 19, 30, 30, 30, 30, 30, 7, 7, 1, 12, 12, 26, 26, 26, 26, 26, 5, 1, 1, 1, 1, 7, 19, 19, 30, 30, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 46, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 192 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114128 none O=C(CC1=CC2=CNN=C2C=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 59, 116, 116, 116, 116, 116, 116, 116, 116, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 59, 59, 116, 116, 116, 116, 116, 22, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 341 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114128 none O=C(CC1=CC2=CNN=C2C=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 26, 26, 26, 116, 116, 116, 161, 201, 201, 201, 201, 201, 116, 116, 26, 5, 5, 1, 1, 1, 1, 1, 11, 26, 26, 26, 26, 116, 161, 161, 201, 201, 26, 26] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 669 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114128 none O=C(CC1=CC2=CNN=C2C=C1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 119, 201, 201, 201, 201, 201, 201, 201, 201, 30, 30, 30, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 30, 119, 119, 201, 201, 201, 201, 201, 53, 30, 30, 30, 30, 7, 4, 4, 2, 2, 30, 30] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 614 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114128 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114128/1 /scratch/stefan/7770410/working/building/REAL300020114128 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1874) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1874 `/scratch/stefan/7770410/working/3D/1874' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC2=CNN=C2C=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114128.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114128/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114128 none O=C(CC1=CC2=CNN=C2C=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 11, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 7, 7, 7, 19, 30, 30, 30, 30, 30, 7, 7, 1, 11, 11, 25, 25, 25, 25, 25, 5, 1, 1, 1, 1, 7, 19, 19, 30, 30, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 46, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 186 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114128 none O=C(CC1=CC2=CNN=C2C=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 58, 116, 116, 116, 116, 116, 116, 116, 116, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 58, 58, 116, 116, 116, 116, 116, 22, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 337 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114128 none O=C(CC1=CC2=CNN=C2C=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 25, 25, 25, 116, 116, 116, 161, 201, 201, 201, 201, 201, 116, 116, 25, 5, 5, 1, 1, 1, 1, 1, 11, 25, 25, 25, 25, 116, 161, 161, 201, 201, 25, 25] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 668 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114128 none O=C(CC1=CC2=CNN=C2C=C1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 118, 201, 201, 201, 201, 201, 201, 201, 201, 30, 30, 30, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 30, 118, 118, 201, 201, 201, 201, 201, 53, 30, 30, 30, 30, 7, 4, 4, 2, 2, 30, 30] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 610 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114128 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114128 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114128/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114128/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114128 Building REAL300020114129 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114129' /scratch/stefan/7770410/working/building/REAL300020114129 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114129 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114129/0 /scratch/stefan/7770410/working/building/REAL300020114129 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1875) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1875 `/scratch/stefan/7770410/working/3D/1875' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=NC=CN2C=C1) `REAL300020114129.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114129 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=NC=CN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 31, 77, 77, 77, 77, 77, 77, 77, 77, 31, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9, 77, 77, 77, 77, 77] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 181 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114129 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=NC=CN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 55, 55, 55, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 55, 94, 201, 201, 201, 201, 201, 201, 201, 201, 94, 55, 55, 55, 55, 12, 6, 6, 4, 4, 55, 55, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 439 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114129 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=NC=CN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 30, 45, 53, 53, 53, 53, 9, 9, 1, 6, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 9, 30, 30, 45, 45, 1, 1, 17, 17, 17, 17, 17] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114129 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=NC=CN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 17, 17, 17, 77, 77, 77, 146, 201, 201, 201, 201, 201, 77, 77, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 17, 17, 17, 17, 77, 146, 146, 201, 201, 17, 17, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 811 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114129 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114129/1 /scratch/stefan/7770410/working/building/REAL300020114129 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1876) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1876 `/scratch/stefan/7770410/working/3D/1876' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=NC=CN2C=C1) `REAL300020114129.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114129 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=NC=CN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 9, 9, 9, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 9, 32, 78, 78, 78, 78, 78, 78, 78, 78, 32, 9, 9, 9, 9, 1, 7, 7, 9, 9, 9, 9, 78, 78, 78, 78, 78] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 183 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114129 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=NC=CN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 55, 55, 55, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 55, 94, 201, 201, 201, 201, 201, 201, 201, 201, 94, 55, 55, 55, 55, 12, 6, 6, 4, 4, 55, 55, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 438 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114129 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=NC=CN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 31, 46, 54, 54, 54, 54, 9, 9, 1, 6, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 9, 31, 31, 46, 46, 1, 1, 17, 17, 17, 17, 17] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114129 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=NC=CN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 17, 17, 17, 78, 78, 78, 147, 201, 201, 201, 201, 201, 78, 78, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 17, 17, 17, 17, 78, 147, 147, 201, 201, 17, 17, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 806 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114129 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114129 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114129/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114129/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114129 Building REAL300020114130 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114130' /scratch/stefan/7770410/working/building/REAL300020114130 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114130 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114130/0 /scratch/stefan/7770410/working/building/REAL300020114130 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1877) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1877 `/scratch/stefan/7770410/working/3D/1877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=NC=CN21) `REAL300020114130.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114130 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=NC=CN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 11, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 11, 30, 91, 91, 91, 91, 91, 91, 91, 91, 30, 11, 11, 11, 11, 1, 5, 5, 7, 7, 11, 11, 91, 91, 91, 91, 91] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 178 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114130 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=NC=CN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 40, 40, 40, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 40, 83, 201, 201, 201, 201, 201, 201, 201, 201, 83, 40, 40, 40, 40, 7, 4, 4, 2, 2, 40, 40, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 402 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114130 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=NC=CN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 27, 40, 40, 40, 40, 40, 11, 11, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 1, 11, 27, 27, 40, 40, 1, 1, 17, 17, 17, 17, 17] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114130 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=NC=CN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 17, 17, 17, 91, 91, 91, 160, 201, 201, 201, 201, 201, 91, 91, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 17, 17, 17, 17, 91, 160, 160, 201, 201, 17, 17, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 758 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114130 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114130/1 /scratch/stefan/7770410/working/building/REAL300020114130 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1878) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1878 `/scratch/stefan/7770410/working/3D/1878' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=NC=CN21) `REAL300020114130.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114130 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=NC=CN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 11, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 11, 30, 92, 92, 92, 92, 92, 92, 92, 92, 30, 11, 11, 11, 11, 1, 5, 5, 7, 7, 11, 11, 92, 92, 92, 92, 92] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 180 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114130 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=NC=CN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 40, 40, 40, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 40, 82, 201, 201, 201, 201, 201, 201, 201, 201, 82, 40, 40, 40, 40, 7, 4, 4, 2, 2, 40, 40, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 402 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114130 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=NC=CN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 27, 40, 40, 40, 40, 40, 11, 11, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 1, 11, 27, 27, 40, 40, 1, 1, 17, 17, 17, 17, 17] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114130 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=NC=CN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 17, 17, 17, 92, 92, 92, 160, 201, 201, 201, 201, 201, 92, 92, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 17, 17, 17, 17, 92, 160, 160, 201, 201, 17, 17, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 753 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114130 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114130 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114130/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114130/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114130 Building REAL300020114131 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114131' /scratch/stefan/7770410/working/building/REAL300020114131 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114131 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114131/0 /scratch/stefan/7770410/working/building/REAL300020114131 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1879) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1879 `/scratch/stefan/7770410/working/3D/1879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2NC=CC2=N1) `REAL300020114131.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114131 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2NC=CC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 1, 1, 13, 57, 85, 85, 85, 85, 85, 85, 85, 85, 57, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13, 85, 85, 85, 85, 85] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 237 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114131 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2NC=CC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 88, 88, 88, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 88, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 88, 88, 88, 88, 13, 6, 6, 4, 4, 88, 88, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 551 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114131 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2NC=CC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 51, 74, 88, 88, 88, 88, 13, 13, 1, 6, 14, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 13, 51, 51, 74, 74, 1, 1, 14, 14, 14, 14, 14] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 355 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114131 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2NC=CC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 14, 14, 14, 85, 85, 85, 170, 201, 201, 201, 201, 201, 85, 85, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 14, 14, 14, 14, 85, 170, 170, 201, 201, 14, 14, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 729 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114131 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114131/1 /scratch/stefan/7770410/working/building/REAL300020114131 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1880) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1880 `/scratch/stefan/7770410/working/3D/1880' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2NC=CC2=N1) `REAL300020114131.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114131 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2NC=CC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 1, 1, 13, 58, 85, 85, 85, 85, 85, 85, 85, 85, 58, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13, 85, 85, 85, 85, 85] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 238 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114131 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2NC=CC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 88, 88, 88, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 88, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 88, 88, 88, 88, 13, 6, 6, 4, 4, 88, 88, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 551 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114131 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2NC=CC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 51, 74, 88, 88, 88, 88, 13, 13, 1, 6, 13, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 13, 51, 51, 74, 74, 1, 1, 13, 13, 13, 13, 13] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 354 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114131 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2NC=CC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 13, 13, 13, 85, 85, 85, 170, 201, 201, 201, 201, 201, 85, 85, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 13, 13, 13, 13, 85, 170, 170, 201, 201, 13, 13, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 728 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114131 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114131 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114131/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114131/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114131 Building REAL300020114132 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114132' /scratch/stefan/7770410/working/building/REAL300020114132 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114132 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114132/0 /scratch/stefan/7770410/working/building/REAL300020114132 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1881) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1881 `/scratch/stefan/7770410/working/3D/1881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN2N=NN=C2C=C1) `REAL300020114132.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114132 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN2N=NN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 8, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 24, 73, 73, 73, 73, 73, 73, 73, 73, 24, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 73, 73, 73] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 166 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114132 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN2N=NN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 8, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 44, 44, 44, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 44, 79, 201, 201, 201, 201, 201, 201, 201, 201, 79, 44, 44, 44, 44, 11, 6, 6, 4, 4, 44, 44, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 418 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114132 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN2N=NN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 8, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 28, 41, 44, 44, 44, 44, 9, 9, 1, 6, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 9, 28, 28, 41, 41, 1, 1, 19, 19, 19] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114132 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CN2N=NN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 8, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 19, 19, 19, 73, 73, 73, 144, 201, 201, 201, 201, 201, 73, 73, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 19, 19, 19, 19, 73, 144, 144, 201, 201, 19, 19, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 818 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114132 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114132/1 /scratch/stefan/7770410/working/building/REAL300020114132 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1882) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1882 `/scratch/stefan/7770410/working/3D/1882' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN2N=NN=C2C=C1) `REAL300020114132.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114132 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN2N=NN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 8, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 24, 73, 73, 73, 73, 73, 73, 73, 73, 24, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 73, 73, 73] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 166 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114132 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN2N=NN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 8, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 44, 44, 44, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 44, 79, 201, 201, 201, 201, 201, 201, 201, 201, 79, 44, 44, 44, 44, 11, 6, 6, 4, 4, 44, 44, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 418 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114132 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN2N=NN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 8, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 28, 41, 44, 44, 44, 44, 9, 9, 1, 6, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 9, 28, 28, 41, 41, 1, 1, 19, 19, 19] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114132 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CN2N=NN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 8, 8, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 19, 19, 19, 73, 73, 73, 144, 201, 201, 201, 201, 201, 73, 73, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 19, 19, 19, 19, 73, 144, 144, 201, 201, 19, 19, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 818 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114132 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114132 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114132/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114132/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114132 Building REAL300020114133 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114133' /scratch/stefan/7770410/working/building/REAL300020114133 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114133 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114133/0 /scratch/stefan/7770410/working/building/REAL300020114133 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1883) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1883 `/scratch/stefan/7770410/working/3D/1883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020114133.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114133 none CC1=NN(C)C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 31, 31, 25, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 29, 42, 44, 44, 44, 44, 9, 9, 1, 31, 31, 31, 31, 31, 31, 31, 25, 25, 5, 1, 1, 1, 1, 9, 29, 29, 42, 42, 1, 1, 31] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47]) total number of confs: 267 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114133 none CC1=NN(C)C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 105, 105, 96, 25, 25, 25, 9, 9, 9, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 9, 105, 105, 105, 105, 105, 105, 105, 96, 96, 25, 9, 9, 9, 9, 1, 5, 5, 7, 7, 9, 9, 105] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 384 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114133 none CC1=NN(C)C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 16, 16, 16, 31, 31, 31, 105, 105, 105, 171, 201, 201, 201, 201, 201, 105, 105, 31, 1, 2, 2, 2, 2, 2, 2, 3, 3, 16, 31, 31, 31, 31, 105, 171, 171, 201, 201, 31, 31, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 47, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 721 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114133 none CC1=NN(C)C(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 193, 82, 82, 82, 44, 44, 44, 9, 9, 9, 6, 4, 1, 1, 1, 1, 1, 1, 9, 9, 44, 201, 201, 201, 201, 201, 201, 201, 193, 193, 82, 44, 44, 44, 44, 9, 6, 6, 4, 4, 44, 44, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 725 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114133 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114133/1 /scratch/stefan/7770410/working/building/REAL300020114133 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1884) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1884 `/scratch/stefan/7770410/working/3D/1884' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020114133.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114133 none CC1=NN(C)C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 31, 31, 25, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 27, 40, 43, 43, 43, 43, 9, 9, 1, 31, 31, 31, 31, 31, 31, 31, 25, 25, 5, 1, 1, 1, 1, 9, 27, 27, 40, 40, 1, 1, 31] 201 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 46, 45, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47]) total number of confs: 263 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114133 none CC1=NN(C)C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 105, 105, 96, 25, 25, 25, 9, 9, 9, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 9, 105, 105, 105, 105, 105, 105, 105, 96, 96, 25, 9, 9, 9, 9, 1, 5, 5, 7, 7, 9, 9, 105] 201 rigid atoms, others: [40, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 381 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114133 none CC1=NN(C)C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 16, 16, 16, 31, 31, 31, 105, 105, 105, 170, 201, 201, 201, 201, 201, 105, 105, 31, 1, 2, 2, 2, 2, 2, 2, 3, 3, 16, 31, 31, 31, 31, 105, 170, 170, 201, 201, 31, 31, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 47, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 721 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114133 none CC1=NN(C)C(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 193, 82, 82, 82, 44, 44, 44, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 44, 201, 201, 201, 201, 201, 201, 201, 193, 193, 82, 44, 44, 44, 44, 10, 6, 6, 4, 4, 44, 44, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 730 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114133 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114133 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114133/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114133/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114133 Building REAL300020114134 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114134' /scratch/stefan/7770410/working/building/REAL300020114134 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114134 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114134/0 /scratch/stefan/7770410/working/building/REAL300020114134 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1885) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1885 `/scratch/stefan/7770410/working/3D/1885' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN2C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CN=C2C=C1) `REAL300020114134.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114134 none CC1=CN2C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 48, 66, 84, 84, 84, 84, 11, 11, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 11, 48, 48, 66, 66, 1, 1, 20, 20, 20] 201 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 327 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114134 none CC1=CN2C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 105, 40, 40, 40, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 11, 105, 105, 105, 105, 105, 105, 105, 105, 105, 40, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 105, 105, 105] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 241 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114134 none CC1=CN2C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 20, 20, 20, 105, 105, 105, 172, 201, 201, 201, 201, 201, 105, 105, 20, 1, 1, 1, 1, 1, 2, 2, 2, 1, 8, 20, 20, 20, 20, 105, 172, 172, 201, 201, 20, 20, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 45, 46, 47, 24, 25, 26, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 691 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114134 none CC1=CN2C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)=CN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 162, 162, 162, 85, 85, 85, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 85, 201, 201, 201, 201, 201, 201, 201, 201, 201, 162, 85, 85, 85, 85, 17, 6, 6, 4, 4, 85, 85, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 527 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114134 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114134/1 /scratch/stefan/7770410/working/building/REAL300020114134 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1886) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1886 `/scratch/stefan/7770410/working/3D/1886' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN2C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CN=C2C=C1) `REAL300020114134.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114134/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114134 none CC1=CN2C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 48, 66, 84, 84, 84, 84, 11, 11, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 11, 48, 48, 66, 66, 1, 1, 21, 21, 21] 201 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 328 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114134 none CC1=CN2C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 106, 40, 40, 40, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 11, 106, 106, 106, 106, 106, 106, 106, 106, 106, 40, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 106, 106, 106] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 242 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114134 none CC1=CN2C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 21, 21, 21, 106, 106, 106, 173, 201, 201, 201, 201, 201, 106, 106, 21, 1, 1, 1, 1, 1, 2, 2, 2, 1, 8, 21, 21, 21, 21, 106, 173, 173, 201, 201, 21, 21, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 45, 46, 47, 24, 25, 26, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 692 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114134 none CC1=CN2C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)=CN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 162, 162, 162, 86, 86, 86, 19, 19, 19, 6, 4, 1, 1, 1, 1, 1, 1, 19, 19, 86, 201, 201, 201, 201, 201, 201, 201, 201, 201, 162, 86, 86, 86, 86, 19, 6, 6, 4, 4, 86, 86, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 521 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114134 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114134 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114134/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114134/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114134 Building REAL300020114135 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114135' /scratch/stefan/7770410/working/building/REAL300020114135 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114135 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114135/0 /scratch/stefan/7770410/working/building/REAL300020114135 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1887) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1887 `/scratch/stefan/7770410/working/3D/1887' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2OCCOC2=N1) `REAL300020114135.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114135 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2OCCOC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 20, 20, 20, 20, 1, 1, 13, 51, 84, 84, 84, 84, 84, 84, 84, 84, 84, 51, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 84, 84, 84, 84, 84, 84] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 249 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114135 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2OCCOC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [196, 196, 115, 115, 115, 23, 23, 23, 6, 4, 1, 1, 1, 1, 1, 1, 23, 23, 115, 196, 201, 201, 201, 201, 201, 201, 201, 201, 201, 196, 115, 115, 115, 115, 23, 6, 6, 4, 4, 115, 115, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 541 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114135 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2OCCOC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 73, 95, 114, 114, 114, 114, 13, 13, 1, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 13, 73, 73, 95, 95, 1, 1, 17, 17, 17, 17, 17, 17] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 425 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114135 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2OCCOC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 17, 17, 17, 84, 84, 84, 170, 201, 201, 201, 201, 201, 84, 84, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 17, 17, 17, 17, 84, 170, 170, 201, 201, 17, 17, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 722 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114135 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114135/1 /scratch/stefan/7770410/working/building/REAL300020114135 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1888) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1888 `/scratch/stefan/7770410/working/3D/1888' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2OCCOC2=N1) `REAL300020114135.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114135/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114135 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2OCCOC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 21, 21, 21, 21, 1, 1, 13, 53, 83, 83, 83, 83, 83, 83, 83, 83, 83, 53, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 83, 83, 83, 83, 83, 83] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 251 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114135 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2OCCOC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [196, 196, 116, 116, 116, 24, 24, 24, 6, 4, 1, 1, 1, 1, 1, 1, 24, 24, 116, 196, 201, 201, 201, 201, 201, 201, 201, 201, 201, 196, 116, 116, 116, 116, 24, 6, 6, 4, 4, 116, 116, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 540 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114135 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2OCCOC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 71, 92, 113, 113, 113, 113, 13, 13, 1, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 13, 71, 71, 92, 92, 1, 1, 16, 16, 16, 16, 16, 16] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 416 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114135 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2OCCOC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 16, 16, 16, 83, 83, 83, 170, 201, 201, 201, 201, 201, 83, 83, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 83, 170, 170, 201, 201, 16, 16, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 717 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114135 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114135 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114135/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114135/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114135 Building REAL300020114136 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114136' /scratch/stefan/7770410/working/building/REAL300020114136 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114136 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114136/0 /scratch/stefan/7770410/working/building/REAL300020114136 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1889) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1889 `/scratch/stefan/7770410/working/3D/1889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(F)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114136.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114136 none CCC1=CC=C(F)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 19, 19, 19, 19, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 26, 39, 42, 42, 42, 42, 8, 8, 1, 29, 29, 29, 29, 29, 19, 19, 19, 6, 1, 1, 1, 1, 8, 26, 26, 39, 39, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 258 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114136 none CCC1=CC=C(F)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 76, 76, 76, 76, 76, 76, 76, 28, 28, 28, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 8, 111, 111, 111, 111, 111, 76, 76, 76, 28, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 384 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114136 none CCC1=CC=C(F)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 19, 76, 76, 76, 143, 178, 183, 183, 183, 183, 76, 76, 19, 3, 3, 3, 3, 3, 1, 1, 1, 5, 19, 19, 19, 19, 76, 143, 143, 178, 178, 19, 19] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 8, 9, 7, 34, 35] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 670 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114136 none CCC1=CC=C(F)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 183, 183, 183, 183, 183, 183, 183, 82, 82, 82, 42, 42, 42, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 42, 201, 201, 201, 201, 201, 183, 183, 183, 82, 42, 42, 42, 42, 10, 6, 6, 4, 4, 42, 42] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 509 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114136 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114136/1 /scratch/stefan/7770410/working/building/REAL300020114136 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1890) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1890 `/scratch/stefan/7770410/working/3D/1890' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(F)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114136.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114136 none CCC1=CC=C(F)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 19, 19, 19, 19, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 27, 40, 43, 43, 43, 43, 8, 8, 1, 29, 29, 29, 29, 29, 19, 19, 19, 6, 1, 1, 1, 1, 8, 27, 27, 40, 40, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 47, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 261 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114136 none CCC1=CC=C(F)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 76, 76, 76, 76, 76, 76, 76, 28, 28, 28, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 8, 112, 112, 112, 112, 112, 76, 76, 76, 28, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 390 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114136 none CCC1=CC=C(F)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 19, 76, 76, 76, 143, 178, 183, 183, 183, 183, 76, 76, 19, 3, 3, 3, 3, 3, 1, 1, 1, 5, 19, 19, 19, 19, 76, 143, 143, 178, 178, 19, 19] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 8, 9, 7, 34, 35] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 667 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114136 none CCC1=CC=C(F)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 183, 183, 183, 183, 183, 183, 183, 82, 82, 82, 44, 44, 44, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 44, 201, 201, 201, 201, 201, 183, 183, 183, 82, 44, 44, 44, 44, 11, 6, 6, 4, 4, 44, 44] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 509 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114136 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114136 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114136/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114136/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114136 Building REAL300020114137 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114137' /scratch/stefan/7770410/working/building/REAL300020114137 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114137 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114137/0 /scratch/stefan/7770410/working/building/REAL300020114137 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1891) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1891 `/scratch/stefan/7770410/working/3D/1891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN2N=CC=C12) `REAL300020114137.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114137 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN2N=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 11, 26, 88, 88, 88, 88, 88, 88, 88, 88, 26, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 88, 88, 88, 88, 88] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 178 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114137 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN2N=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 42, 42, 42, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 42, 71, 201, 201, 201, 201, 201, 201, 201, 201, 71, 42, 42, 42, 42, 8, 4, 4, 2, 2, 42, 42, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 385 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114137 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN2N=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 29, 42, 42, 42, 42, 42, 11, 11, 1, 6, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 29, 29, 42, 42, 1, 1, 22, 22, 22, 22, 22] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114137 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN2N=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 22, 22, 22, 88, 88, 88, 155, 201, 201, 201, 201, 201, 88, 88, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 22, 22, 22, 22, 88, 155, 155, 201, 201, 22, 22, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 777 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114137 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114137/1 /scratch/stefan/7770410/working/building/REAL300020114137 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1892) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1892 `/scratch/stefan/7770410/working/3D/1892' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN2N=CC=C12) `REAL300020114137.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114137 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN2N=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 11, 26, 88, 88, 88, 88, 88, 88, 88, 88, 26, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 88, 88, 88, 88, 88] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 178 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114137 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN2N=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 42, 42, 42, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 42, 71, 201, 201, 201, 201, 201, 201, 201, 201, 71, 42, 42, 42, 42, 8, 4, 4, 2, 2, 42, 42, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 385 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114137 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN2N=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 29, 42, 42, 42, 42, 42, 11, 11, 1, 6, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 29, 29, 42, 42, 1, 1, 22, 22, 22, 22, 22] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114137 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN2N=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 22, 22, 22, 88, 88, 88, 155, 201, 201, 201, 201, 201, 88, 88, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 22, 22, 22, 22, 88, 155, 155, 201, 201, 22, 22, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 777 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114137 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114137 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114137/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114137/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114137 Building REAL300020114138 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114138' /scratch/stefan/7770410/working/building/REAL300020114138 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114138 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114138/0 /scratch/stefan/7770410/working/building/REAL300020114138 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1893) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1893 `/scratch/stefan/7770410/working/3D/1893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2CC(=O)NC2=NC=C1) `REAL300020114138.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114138 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2CC(=O)NC2=NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 1, 11, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 6, 13, 24, 24, 24, 24, 24, 24, 24, 24, 24, 13, 6, 6, 6, 6, 1, 5, 5, 7, 7, 6, 6, 24, 24, 24, 24, 24] 30 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114138 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2CC(=O)NC2=NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 1, 11, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 11, 11, 11, 8, 8, 8, 5, 2, 1, 1, 1, 1, 1, 1, 8, 8, 11, 18, 30, 30, 30, 30, 30, 30, 30, 30, 30, 18, 11, 11, 11, 11, 8, 5, 5, 2, 2, 11, 11, 30, 30, 30, 30, 30] 30 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 80 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114138 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2CC(=O)NC2=NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 1, 11, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 9, 11, 11, 11, 11, 11, 6, 6, 1, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 6, 9, 9, 11, 11, 1, 1, 19, 19, 19, 19, 19] 30 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114138 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2CC(=O)NC2=NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 1, 11, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 19, 19, 19, 24, 24, 24, 30, 30, 30, 30, 30, 30, 24, 24, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 19, 19, 19, 19, 24, 30, 30, 30, 30, 19, 19, 1, 1, 1, 1, 1] 30 rigid atoms, others: [1, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 93 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114138 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114138/1 /scratch/stefan/7770410/working/building/REAL300020114138 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1894) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1894 `/scratch/stefan/7770410/working/3D/1894' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2CC(=O)NC2=NC=C1) `REAL300020114138.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114138/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114138 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2CC(=O)NC2=NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 1, 11, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 6, 13, 24, 24, 24, 24, 24, 24, 24, 24, 24, 13, 6, 6, 6, 6, 1, 5, 5, 7, 7, 6, 6, 24, 24, 24, 24, 24] 30 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114138 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2CC(=O)NC2=NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 1, 11, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 11, 11, 11, 8, 8, 8, 5, 2, 1, 1, 1, 1, 1, 1, 8, 8, 11, 18, 30, 30, 30, 30, 30, 30, 30, 30, 30, 18, 11, 11, 11, 11, 8, 5, 5, 2, 2, 11, 11, 30, 30, 30, 30, 30] 30 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 80 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114138 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2CC(=O)NC2=NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 1, 11, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 9, 11, 11, 11, 11, 11, 6, 6, 1, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 6, 9, 9, 11, 11, 1, 1, 19, 19, 19, 19, 19] 30 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114138 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2CC(=O)NC2=NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 1, 11, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 19, 19, 19, 24, 24, 24, 30, 30, 30, 30, 30, 30, 24, 24, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 19, 19, 19, 19, 24, 30, 30, 30, 30, 19, 19, 1, 1, 1, 1, 1] 30 rigid atoms, others: [1, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 93 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114138 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114138 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114138/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114138/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114138 Building REAL300020114139 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114139' /scratch/stefan/7770410/working/building/REAL300020114139 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114139 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114139/0 /scratch/stefan/7770410/working/building/REAL300020114139 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1895) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1895 `/scratch/stefan/7770410/working/3D/1895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN=C1C1CC1) `REAL300020114139.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114139 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN=C1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 13, 56, 157, 157, 157, 157, 157, 157, 167, 167, 56, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 157, 157, 157, 167, 167, 167, 167, 167] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 347 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114139 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN=C1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 6, 19, 19, 50, 50, 50, 167, 167, 167, 191, 201, 201, 201, 201, 201, 167, 167, 50, 6, 6, 6, 6, 6, 1, 1, 1, 1, 19, 50, 50, 50, 50, 167, 191, 191, 201, 201, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 46, 47, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 476 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114139 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN=C1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 31, 31, 31, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 31, 87, 193, 193, 193, 193, 193, 193, 201, 201, 87, 31, 31, 31, 31, 7, 4, 4, 2, 2, 31, 31, 193, 193, 193, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 428 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114139 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN=C1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 24, 32, 32, 32, 32, 32, 13, 13, 1, 6, 34, 34, 34, 34, 34, 34, 50, 50, 6, 1, 1, 1, 1, 13, 24, 24, 32, 32, 1, 1, 34, 34, 34, 50, 50, 50, 50, 50] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114139 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN=C1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 34, 34, 34, 157, 157, 157, 181, 193, 193, 193, 193, 193, 157, 157, 34, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 34, 34, 34, 34, 157, 181, 181, 193, 193, 34, 34, 1, 1, 1, 6, 6, 6, 6, 6] 201 rigid atoms, others: [1, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47]) total number of confs: 454 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114139 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114139/1 /scratch/stefan/7770410/working/building/REAL300020114139 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1896) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1896 `/scratch/stefan/7770410/working/3D/1896' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN=C1C1CC1) `REAL300020114139.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114139 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN=C1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 13, 56, 157, 157, 157, 157, 157, 157, 168, 168, 56, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 157, 157, 157, 168, 168, 168, 168, 168] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 351 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114139 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN=C1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 6, 19, 19, 51, 51, 51, 168, 168, 168, 192, 201, 201, 201, 201, 201, 168, 168, 51, 6, 6, 6, 6, 6, 1, 1, 1, 1, 19, 51, 51, 51, 51, 168, 192, 192, 201, 201, 51, 51, 6, 6, 6, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 46, 47, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 472 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114139 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN=C1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 32, 32, 32, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 32, 88, 192, 192, 192, 192, 192, 192, 201, 201, 88, 32, 32, 32, 32, 7, 4, 4, 2, 2, 32, 32, 192, 192, 192, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 431 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114139 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN=C1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 24, 32, 32, 32, 32, 32, 13, 13, 1, 6, 34, 34, 34, 34, 34, 34, 51, 51, 6, 1, 1, 1, 1, 13, 24, 24, 32, 32, 1, 1, 34, 34, 34, 51, 51, 51, 51, 51] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114139 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN=C1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 34, 34, 34, 157, 157, 157, 181, 192, 192, 192, 192, 192, 157, 157, 34, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 34, 34, 34, 34, 157, 181, 181, 192, 192, 34, 34, 1, 1, 1, 6, 6, 6, 6, 6] 201 rigid atoms, others: [1, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47]) total number of confs: 448 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114139 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114139 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114139/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114139/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114139 Building REAL300020114140 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114140' /scratch/stefan/7770410/working/building/REAL300020114140 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114140 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114140/0 /scratch/stefan/7770410/working/building/REAL300020114140 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1897) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1897 `/scratch/stefan/7770410/working/3D/1897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2OCCCN2N=C1) `REAL300020114140.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114140 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2OCCCN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 5, 5, 5, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 9, 9, 9, 1, 1, 1, 1, 1, 9, 14, 21, 21, 21, 21, 1, 1, 9, 31, 81, 81, 81, 81, 81, 81, 81, 81, 31, 9, 9, 9, 9, 1, 9, 9, 14, 14, 9, 9, 81, 81, 81, 81, 81, 81, 81] 178 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 221 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114140 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2OCCCN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 5, 5, 5, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [149, 149, 91, 91, 91, 30, 30, 30, 6, 4, 1, 1, 1, 1, 1, 1, 30, 30, 91, 149, 178, 178, 178, 178, 178, 178, 178, 178, 149, 91, 91, 91, 91, 30, 6, 6, 4, 4, 91, 91, 178, 178, 178, 178, 178, 178, 178] 178 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 466 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114140 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2OCCCN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 5, 5, 5, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 46, 61, 80, 80, 80, 80, 9, 9, 1, 6, 28, 28, 28, 28, 28, 28, 28, 28, 6, 1, 1, 1, 1, 9, 46, 46, 61, 61, 1, 1, 28, 28, 28, 28, 28, 28, 28] 178 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 309 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114140 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2OCCCN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 5, 5, 5, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 28, 28, 28, 81, 81, 81, 156, 178, 178, 178, 178, 178, 81, 81, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 28, 28, 28, 28, 81, 156, 156, 178, 178, 28, 28, 1, 1, 1, 1, 1, 1, 1] 178 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 638 number of broken/clashed sets: 3 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114140 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114140/1 /scratch/stefan/7770410/working/building/REAL300020114140 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1898) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1898 `/scratch/stefan/7770410/working/3D/1898' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2OCCCN2N=C1) `REAL300020114140.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114140 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2OCCCN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 5, 5, 5, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 9, 9, 9, 1, 1, 1, 1, 1, 9, 14, 21, 21, 21, 21, 1, 1, 9, 31, 81, 81, 81, 81, 81, 81, 81, 81, 31, 9, 9, 9, 9, 1, 9, 9, 14, 14, 9, 9, 81, 81, 81, 81, 81, 81, 81] 178 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 221 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114140 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2OCCCN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 5, 5, 5, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [150, 150, 92, 92, 92, 30, 30, 30, 6, 4, 1, 1, 1, 1, 1, 1, 30, 30, 92, 150, 178, 178, 178, 178, 178, 178, 178, 178, 150, 92, 92, 92, 92, 30, 6, 6, 4, 4, 92, 92, 178, 178, 178, 178, 178, 178, 178] 178 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 466 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114140 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2OCCCN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 5, 5, 5, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 46, 61, 80, 80, 80, 80, 9, 9, 1, 6, 28, 28, 28, 28, 28, 28, 28, 28, 6, 1, 1, 1, 1, 9, 46, 46, 61, 61, 1, 1, 28, 28, 28, 28, 28, 28, 28] 178 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 309 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114140 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2OCCCN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 5, 5, 5, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 28, 28, 28, 81, 81, 81, 156, 178, 178, 178, 178, 178, 81, 81, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 28, 28, 28, 28, 81, 156, 156, 178, 178, 28, 28, 1, 1, 1, 1, 1, 1, 1] 178 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 638 number of broken/clashed sets: 3 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114140 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114140 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114140/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114140/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114140 Building REAL300020114141 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114141' /scratch/stefan/7770410/working/building/REAL300020114141 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114141 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114141/0 /scratch/stefan/7770410/working/building/REAL300020114141 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1899) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1899 `/scratch/stefan/7770410/working/3D/1899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC(OC)=N1) `REAL300020114141.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114141 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC(OC)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 50, 68, 82, 82, 82, 82, 12, 12, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 12, 50, 50, 68, 68, 1, 1, 11, 11, 11, 11] 201 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48]) total number of confs: 315 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114141 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC(OC)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 77, 43, 43, 43, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 12, 77, 77, 77, 77, 77, 77, 77, 77, 77, 43, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 77, 77, 77, 77] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 224 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114141 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC(OC)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 77, 77, 77, 152, 201, 201, 201, 201, 201, 77, 77, 11, 1, 1, 1, 2, 1, 2, 2, 2, 1, 3, 11, 11, 11, 11, 77, 152, 152, 201, 201, 11, 11, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 45, 24, 25, 26, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48]) total number of confs: 759 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114141 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CC(OC)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 125, 125, 125, 86, 86, 86, 20, 20, 20, 6, 4, 1, 1, 1, 1, 1, 1, 20, 20, 86, 201, 201, 201, 201, 201, 201, 201, 201, 201, 125, 86, 86, 86, 86, 20, 6, 6, 4, 4, 86, 86, 201, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 500 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114141 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114141/1 /scratch/stefan/7770410/working/building/REAL300020114141 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1900) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1900 `/scratch/stefan/7770410/working/3D/1900' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC(OC)=N1) `REAL300020114141.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114141 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC(OC)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 50, 68, 82, 82, 82, 82, 12, 12, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 12, 50, 50, 68, 68, 1, 1, 11, 11, 11, 11] 201 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48]) total number of confs: 315 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114141 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC(OC)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 77, 43, 43, 43, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 12, 77, 77, 77, 77, 77, 77, 77, 77, 77, 43, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 77, 77, 77, 77] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 224 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114141 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC(OC)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 77, 77, 77, 151, 201, 201, 201, 201, 201, 77, 77, 11, 1, 1, 1, 2, 1, 2, 2, 2, 1, 3, 11, 11, 11, 11, 77, 151, 151, 201, 201, 11, 11, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 45, 24, 25, 26, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48]) total number of confs: 756 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114141 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CC(OC)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 125, 125, 125, 86, 86, 86, 20, 20, 20, 6, 4, 1, 1, 1, 1, 1, 1, 20, 20, 86, 201, 201, 201, 201, 201, 201, 201, 201, 201, 125, 86, 86, 86, 86, 20, 6, 6, 4, 4, 86, 86, 201, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 500 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114141 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114141 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114141/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114141/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114141 Building REAL300020114142 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114142' /scratch/stefan/7770410/working/building/REAL300020114142 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114142 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114142/0 /scratch/stefan/7770410/working/building/REAL300020114142 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1901) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1901 `/scratch/stefan/7770410/working/3D/1901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CO1) `REAL300020114142.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114142 none CCOC1=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 13, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 39, 57, 63, 63, 63, 63, 13, 13, 1, 6, 6, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 13, 39, 39, 57, 57, 1, 1, 6] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 299 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114142 none CCOC1=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 85, 50, 50, 50, 50, 50, 50, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 50, 50, 105, 105, 105, 105, 105, 50, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 50] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 332 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114142 none CCOC1=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 115, 150, 155, 155, 155, 155, 50, 50, 6, 1, 1, 8, 8, 8, 8, 8, 1, 6, 6, 6, 6, 50, 115, 115, 150, 150, 6, 6, 1] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 44, 25, 26] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 609 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114142 none CCOC1=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 155, 155, 155, 155, 155, 155, 62, 62, 62, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 62, 155, 155, 201, 201, 201, 201, 201, 155, 62, 62, 62, 62, 11, 6, 6, 4, 4, 62, 62, 155] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 521 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114142 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114142/1 /scratch/stefan/7770410/working/building/REAL300020114142 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1902) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1902 `/scratch/stefan/7770410/working/3D/1902' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CO1) `REAL300020114142.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114142 none CCOC1=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 13, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 40, 58, 64, 64, 64, 64, 13, 13, 1, 6, 6, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 13, 40, 40, 58, 58, 1, 1, 6] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 302 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114142 none CCOC1=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 85, 50, 50, 50, 50, 50, 50, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 50, 50, 105, 105, 105, 105, 105, 50, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 50] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 332 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114142 none CCOC1=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 117, 151, 156, 156, 156, 156, 50, 50, 6, 1, 1, 8, 8, 8, 8, 8, 1, 6, 6, 6, 6, 50, 117, 117, 151, 151, 6, 6, 1] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 44, 25, 26] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 609 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114142 none CCOC1=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 155, 155, 155, 155, 155, 155, 61, 61, 61, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 61, 155, 155, 201, 201, 201, 201, 201, 155, 61, 61, 61, 61, 10, 6, 6, 4, 4, 61, 61, 155] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 523 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114142 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114142 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114142/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114142/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114142 Building REAL300020114143 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114143' /scratch/stefan/7770410/working/building/REAL300020114143 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114143 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114143/0 /scratch/stefan/7770410/working/building/REAL300020114143 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1903) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1903 `/scratch/stefan/7770410/working/3D/1903' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=COC(C(F)(F)F)=N1) `REAL300020114143.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114143 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=COC(C(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 5, 15, 15, 15, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 13, 59, 120, 120, 120, 120, 120, 120, 120, 120, 59, 13, 13, 13, 13, 1, 7, 7, 9, 9, 13, 13, 120] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 286 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114143 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=COC(C(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 5, 15, 15, 15, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [168, 168, 61, 61, 61, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 61, 168, 201, 201, 201, 201, 201, 201, 201, 201, 168, 61, 61, 61, 61, 11, 6, 6, 4, 4, 61, 61, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 537 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114143 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=COC(C(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 5, 15, 15, 15, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 39, 57, 61, 61, 61, 61, 13, 13, 1, 6, 24, 24, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 13, 39, 39, 57, 57, 1, 1, 24] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40]) total number of confs: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114143 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=COC(C(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 5, 15, 15, 15, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 24, 24, 24, 120, 120, 120, 178, 201, 201, 201, 201, 201, 120, 120, 24, 1, 1, 1, 1, 1, 2, 2, 2, 1, 10, 24, 24, 24, 24, 120, 178, 178, 201, 201, 24, 24, 1] 201 rigid atoms, others: [1, 40, 19, 20, 21, 22, 23, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 610 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114143 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114143/1 /scratch/stefan/7770410/working/building/REAL300020114143 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1904) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1904 `/scratch/stefan/7770410/working/3D/1904' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=COC(C(F)(F)F)=N1) `REAL300020114143.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114143 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=COC(C(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 5, 15, 15, 15, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 13, 59, 120, 120, 120, 120, 120, 120, 120, 120, 59, 13, 13, 13, 13, 1, 7, 7, 9, 9, 13, 13, 120] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 287 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114143 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=COC(C(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 5, 15, 15, 15, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [171, 171, 62, 62, 62, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 62, 171, 201, 201, 201, 201, 201, 201, 201, 201, 171, 62, 62, 62, 62, 11, 6, 6, 4, 4, 62, 62, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 538 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114143 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=COC(C(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 5, 15, 15, 15, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 39, 57, 62, 62, 62, 62, 13, 13, 1, 6, 24, 24, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 13, 39, 39, 57, 57, 1, 1, 24] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40]) total number of confs: 281 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114143 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=COC(C(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 12, 1, 5, 15, 15, 15, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 24, 24, 24, 120, 120, 120, 179, 201, 201, 201, 201, 201, 120, 120, 24, 1, 1, 1, 1, 1, 2, 2, 2, 1, 10, 24, 24, 24, 24, 120, 179, 179, 201, 201, 24, 24, 1] 201 rigid atoms, others: [1, 40, 19, 20, 21, 22, 23, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 609 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114143 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114143 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114143/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114143/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114143 Building REAL300020114144 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114144' /scratch/stefan/7770410/working/building/REAL300020114144 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114144 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114144/0 /scratch/stefan/7770410/working/building/REAL300020114144 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1905) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1905 `/scratch/stefan/7770410/working/3D/1905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=CNC2=NC=N1) `REAL300020114144.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114144 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=CNC2=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 1, 1, 13, 61, 133, 133, 133, 133, 133, 133, 133, 133, 61, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13, 133, 133, 133, 133] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 301 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114144 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=CNC2=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [160, 160, 52, 52, 52, 10, 10, 10, 4, 2, 1, 1, 1, 1, 1, 1, 10, 10, 52, 160, 201, 201, 201, 201, 201, 201, 201, 201, 160, 52, 52, 52, 52, 10, 4, 4, 2, 2, 52, 52, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 494 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114144 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=CNC2=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 37, 52, 52, 52, 52, 52, 13, 13, 1, 6, 35, 35, 35, 35, 35, 35, 35, 35, 6, 1, 1, 1, 1, 13, 37, 37, 52, 52, 1, 1, 35, 35, 35, 35] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114144 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=CNC2=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 35, 35, 35, 133, 133, 133, 178, 201, 201, 201, 201, 201, 133, 133, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 35, 35, 35, 35, 133, 178, 178, 201, 201, 35, 35, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 588 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114144 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114144/1 /scratch/stefan/7770410/working/building/REAL300020114144 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1906) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1906 `/scratch/stefan/7770410/working/3D/1906' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=CNC2=NC=N1) `REAL300020114144.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114144 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=CNC2=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 1, 1, 13, 61, 134, 134, 134, 134, 134, 134, 134, 134, 61, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13, 134, 134, 134, 134] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 301 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114144 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=CNC2=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [159, 159, 52, 52, 52, 10, 10, 10, 4, 2, 1, 1, 1, 1, 1, 1, 10, 10, 52, 159, 201, 201, 201, 201, 201, 201, 201, 201, 159, 52, 52, 52, 52, 10, 4, 4, 2, 2, 52, 52, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 490 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114144 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=CNC2=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 37, 52, 52, 52, 52, 52, 13, 13, 1, 6, 35, 35, 35, 35, 35, 35, 35, 35, 6, 1, 1, 1, 1, 13, 37, 37, 52, 52, 1, 1, 35, 35, 35, 35] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114144 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=CNC2=NC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 35, 35, 35, 134, 134, 134, 178, 201, 201, 201, 201, 201, 134, 134, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 35, 35, 35, 35, 134, 178, 178, 201, 201, 35, 35, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 583 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114144 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114144 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114144/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114144/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114144 Building REAL300020114145 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114145' /scratch/stefan/7770410/working/building/REAL300020114145 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114145 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114145/0 /scratch/stefan/7770410/working/building/REAL300020114145 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1907) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1907 `/scratch/stefan/7770410/working/3D/1907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1C) `REAL300020114145.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114145 none COC1=CC(C)=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 27, 27, 27, 27, 27, 27, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 33, 42, 54, 54, 54, 54, 7, 7, 1, 27, 27, 53, 53, 53, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 7, 33, 33, 42, 42, 1, 1, 27, 27, 27] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50, 51]) total number of confs: 261 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114145 none COC1=CC(C)=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 82, 82, 82, 82, 82, 82, 24, 24, 24, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 7, 82, 82, 117, 117, 117, 82, 82, 82, 82, 82, 24, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7, 82, 82, 82] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 251 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114145 none COC1=CC(C)=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 27, 27, 27, 82, 82, 82, 156, 189, 201, 201, 201, 201, 82, 82, 27, 1, 1, 4, 4, 4, 1, 2, 2, 2, 1, 7, 27, 27, 27, 27, 82, 156, 156, 189, 189, 27, 27, 2, 2, 2] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 36, 27, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 712 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114145 none COC1=CC(C)=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 111, 111, 111, 61, 61, 61, 21, 21, 21, 7, 4, 1, 1, 1, 1, 1, 1, 21, 21, 61, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 111, 61, 61, 61, 61, 21, 7, 7, 4, 4, 61, 61, 201, 201, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 460 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114145 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114145/1 /scratch/stefan/7770410/working/building/REAL300020114145 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1908) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1908 `/scratch/stefan/7770410/working/3D/1908' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1C) `REAL300020114145.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114145 none COC1=CC(C)=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 27, 27, 27, 27, 27, 27, 6, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 33, 42, 54, 54, 54, 54, 7, 7, 1, 27, 27, 51, 51, 51, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 7, 33, 33, 42, 42, 1, 1, 27, 27, 27] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49, 50, 51]) total number of confs: 259 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114145 none COC1=CC(C)=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 80, 80, 80, 80, 80, 80, 23, 23, 23, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 7, 80, 80, 114, 114, 114, 80, 80, 80, 80, 80, 23, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7, 80, 80, 80] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 243 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114145 none COC1=CC(C)=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 27, 27, 27, 80, 80, 80, 154, 189, 201, 201, 201, 201, 80, 80, 27, 1, 1, 4, 4, 4, 1, 2, 2, 2, 1, 7, 27, 27, 27, 27, 80, 154, 154, 189, 189, 27, 27, 2, 2, 2] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 36, 27, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 722 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114145 none COC1=CC(C)=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 110, 110, 110, 61, 61, 61, 22, 22, 22, 7, 4, 1, 1, 1, 1, 1, 1, 22, 22, 61, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 110, 61, 61, 61, 61, 22, 7, 7, 4, 4, 61, 61, 201, 201, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 457 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114145 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114145 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114145/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114145/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114145 Building REAL300020114146 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114146' /scratch/stefan/7770410/working/building/REAL300020114146 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114146 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114146/0 /scratch/stefan/7770410/working/building/REAL300020114146 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1909) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1909 `/scratch/stefan/7770410/working/3D/1909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CN=CC=C2O1) `REAL300020114146.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114146 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CN=CC=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 8, 8, 8, 1, 1, 1, 1, 1, 9, 13, 17, 17, 17, 17, 1, 1, 8, 29, 63, 63, 63, 63, 63, 63, 63, 63, 29, 8, 8, 8, 8, 1, 9, 9, 13, 13, 8, 8, 63, 63, 63, 63] 143 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 182 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114146 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CN=CC=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 66, 66, 66, 23, 23, 23, 6, 4, 1, 1, 1, 1, 1, 1, 23, 23, 66, 119, 143, 143, 143, 143, 143, 143, 143, 143, 119, 66, 66, 66, 66, 23, 6, 6, 4, 4, 66, 66, 143, 143, 143, 143] 143 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 379 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114146 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CN=CC=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 36, 48, 61, 61, 61, 61, 8, 8, 1, 6, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 8, 36, 36, 48, 48, 1, 1, 21, 21, 21, 21] 143 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114146 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CN=CC=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 21, 21, 21, 63, 63, 63, 119, 143, 143, 143, 143, 143, 63, 63, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 21, 21, 21, 21, 63, 119, 119, 143, 143, 21, 21, 1, 1, 1, 1] 143 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 524 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114146 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114146/1 /scratch/stefan/7770410/working/building/REAL300020114146 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1910) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1910 `/scratch/stefan/7770410/working/3D/1910' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CN=CC=C2O1) `REAL300020114146.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114146 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CN=CC=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 8, 8, 8, 1, 1, 1, 1, 1, 9, 13, 17, 17, 17, 17, 1, 1, 8, 29, 63, 63, 63, 63, 63, 63, 63, 63, 29, 8, 8, 8, 8, 1, 9, 9, 13, 13, 8, 8, 63, 63, 63, 63] 143 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 182 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114146 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CN=CC=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 66, 66, 66, 23, 23, 23, 6, 4, 1, 1, 1, 1, 1, 1, 23, 23, 66, 119, 143, 143, 143, 143, 143, 143, 143, 143, 119, 66, 66, 66, 66, 23, 6, 6, 4, 4, 66, 66, 143, 143, 143, 143] 143 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 379 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114146 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CN=CC=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 36, 48, 61, 61, 61, 61, 8, 8, 1, 6, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 8, 36, 36, 48, 48, 1, 1, 21, 21, 21, 21] 143 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114146 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CN=CC=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 21, 21, 21, 63, 63, 63, 119, 143, 143, 143, 143, 143, 63, 63, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 21, 21, 21, 21, 63, 119, 119, 143, 143, 21, 21, 1, 1, 1, 1] 143 rigid atoms, others: [1, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 524 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114146 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114146 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114146/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114146/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114146 Building REAL300020114147 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114147' /scratch/stefan/7770410/working/building/REAL300020114147 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114147 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114147/0 /scratch/stefan/7770410/working/building/REAL300020114147 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1911) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1911 `/scratch/stefan/7770410/working/3D/1911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CN=CN2C=C1) `REAL300020114147.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114147 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CN=CN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 25, 73, 73, 73, 73, 73, 73, 73, 73, 25, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 73, 73, 73, 73, 73] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 168 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114147 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CN=CN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 49, 49, 49, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 49, 82, 201, 201, 201, 201, 201, 201, 201, 201, 82, 49, 49, 49, 49, 10, 6, 6, 4, 4, 49, 49, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 417 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114147 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CN=CN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 29, 43, 48, 48, 48, 48, 9, 9, 1, 5, 15, 15, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 9, 29, 29, 43, 43, 1, 1, 15, 15, 15, 15, 15] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114147 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=CN=CN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 15, 15, 15, 73, 73, 73, 149, 201, 201, 201, 201, 201, 73, 73, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 73, 149, 149, 201, 201, 15, 15, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 813 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114147 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114147/1 /scratch/stefan/7770410/working/building/REAL300020114147 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1912) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1912 `/scratch/stefan/7770410/working/3D/1912' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CN=CN2C=C1) `REAL300020114147.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114147 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CN=CN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 25, 73, 73, 73, 73, 73, 73, 73, 73, 25, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 73, 73, 73, 73, 73] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 168 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114147 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CN=CN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 48, 48, 48, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 48, 81, 201, 201, 201, 201, 201, 201, 201, 201, 81, 48, 48, 48, 48, 11, 6, 6, 4, 4, 48, 48, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 416 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114147 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CN=CN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 29, 43, 48, 48, 48, 48, 9, 9, 1, 5, 15, 15, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 9, 29, 29, 43, 43, 1, 1, 15, 15, 15, 15, 15] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114147 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=CN=CN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 15, 15, 15, 73, 73, 73, 149, 201, 201, 201, 201, 201, 73, 73, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 73, 149, 149, 201, 201, 15, 15, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 813 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114147 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114147 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114147/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114147/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114147 Building REAL300020114148 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114148' /scratch/stefan/7770410/working/building/REAL300020114148 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114148 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114148/0 /scratch/stefan/7770410/working/building/REAL300020114148 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1913) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1913 `/scratch/stefan/7770410/working/3D/1913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NNC(=O)[N-]C1=O) `REAL300020114148.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114148 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NNC(=O)[N-]C1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 11, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 11, 11, 11, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 11, 43, 83, 83, 83, 83, 83, 83, 83, 43, 11, 11, 11, 11, 1, 3, 3, 3, 3, 11, 11, 83] 84 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 183 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114148 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NNC(=O)[N-]C1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 11, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 15, 15, 15, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 50, 84, 84, 84, 84, 84, 84, 84, 50, 15, 15, 15, 15, 3, 3, 3, 1, 1, 15, 15, 84] 84 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 190 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114148 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NNC(=O)[N-]C1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 11, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 15, 15, 15, 15, 15, 15, 11, 11, 1, 6, 36, 36, 36, 36, 36, 36, 36, 6, 1, 1, 1, 1, 11, 15, 15, 15, 15, 1, 1, 36] 84 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114148 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NNC(=O)[N-]C1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 11, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 36, 36, 36, 83, 83, 83, 84, 84, 84, 84, 84, 84, 83, 83, 36, 1, 1, 1, 1, 1, 1, 1, 1, 12, 36, 36, 36, 36, 83, 84, 84, 84, 84, 36, 36, 1] 84 rigid atoms, others: [1, 39, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 166 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114148 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114148/1 /scratch/stefan/7770410/working/building/REAL300020114148 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1914) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1914 `/scratch/stefan/7770410/working/3D/1914' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NNC(=O)[N-]C1=O) `REAL300020114148.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114148/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114148 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NNC(=O)[N-]C1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 11, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 11, 11, 11, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 11, 42, 80, 80, 80, 80, 80, 80, 80, 42, 11, 11, 11, 11, 1, 3, 3, 3, 3, 11, 11, 80] 82 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 178 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114148 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NNC(=O)[N-]C1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 11, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 15, 15, 15, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 48, 82, 82, 82, 82, 82, 82, 82, 48, 15, 15, 15, 15, 3, 3, 3, 1, 1, 15, 15, 82] 82 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 186 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114148 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NNC(=O)[N-]C1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 11, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 15, 15, 15, 15, 15, 15, 11, 11, 1, 6, 34, 34, 34, 34, 34, 34, 34, 6, 1, 1, 1, 1, 11, 15, 15, 15, 15, 1, 1, 34] 82 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114148 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NNC(=O)[N-]C1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 1, 11, 8, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 34, 34, 34, 80, 80, 80, 82, 82, 82, 82, 82, 82, 80, 80, 34, 1, 1, 1, 1, 1, 1, 1, 1, 12, 34, 34, 34, 34, 80, 82, 82, 82, 82, 34, 34, 1] 82 rigid atoms, others: [1, 39, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 166 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114148 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114148 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114148/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114148/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114148 Building REAL300020114149 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114149' /scratch/stefan/7770410/working/building/REAL300020114149 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114149 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114149/0 /scratch/stefan/7770410/working/building/REAL300020114149 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1915) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1915 `/scratch/stefan/7770410/working/3D/1915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114149.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114149 none CC1=NN=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 9, 10, 10, 10, 10, 10, 6, 6, 1, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 6, 9, 9, 10, 10, 1, 1] 20 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114149 none CC1=NN=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 9, 9, 9, 6, 6, 6, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 6, 16, 16, 16, 16, 16, 9, 6, 6, 6, 6, 1, 5, 5, 7, 7, 6, 6] 20 rigid atoms, others: [36, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 63 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114149 none CC1=NN=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 15, 15, 15, 16, 16, 16, 20, 20, 20, 20, 20, 20, 16, 16, 15, 2, 2, 2, 1, 1, 9, 15, 15, 15, 15, 16, 20, 20, 20, 20, 15, 15] 20 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114149 none CC1=NN=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 13, 13, 13, 10, 10, 10, 8, 8, 8, 5, 2, 1, 1, 1, 1, 1, 1, 8, 8, 10, 20, 20, 20, 20, 20, 13, 10, 10, 10, 10, 8, 5, 5, 2, 2, 10, 10] 20 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 60 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114149 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114149/1 /scratch/stefan/7770410/working/building/REAL300020114149 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1916) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1916 `/scratch/stefan/7770410/working/3D/1916' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114149.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114149/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114149 none CC1=NN=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 9, 10, 10, 10, 10, 10, 6, 6, 1, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 6, 9, 9, 10, 10, 1, 1] 20 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114149 none CC1=NN=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 9, 9, 9, 6, 6, 6, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 6, 16, 16, 16, 16, 16, 9, 6, 6, 6, 6, 1, 5, 5, 7, 7, 6, 6] 20 rigid atoms, others: [36, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 63 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114149 none CC1=NN=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 15, 15, 15, 16, 16, 16, 20, 20, 20, 20, 20, 20, 16, 16, 15, 2, 2, 2, 1, 1, 9, 15, 15, 15, 15, 16, 20, 20, 20, 20, 15, 15] 20 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114149 none CC1=NN=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 13, 13, 13, 10, 10, 10, 8, 8, 8, 5, 2, 1, 1, 1, 1, 1, 1, 8, 8, 10, 20, 20, 20, 20, 20, 13, 10, 10, 10, 10, 8, 5, 5, 2, 2, 10, 10] 20 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 60 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114149 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114149 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114149/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114149/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114149 Building REAL300020114150 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114150' /scratch/stefan/7770410/working/building/REAL300020114150 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114150 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114150/0 /scratch/stefan/7770410/working/building/REAL300020114150 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1917) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1917 `/scratch/stefan/7770410/working/3D/1917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NC(C2CC2)=C1) `REAL300020114150.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114150 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 10, 10, 10, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 10, 30, 94, 94, 94, 94, 94, 142, 142, 94, 30, 10, 10, 10, 10, 1, 5, 5, 7, 7, 10, 10, 94, 94, 142, 142, 142, 142, 142, 94] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 378 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114150 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 7, 23, 23, 59, 59, 59, 142, 142, 142, 181, 201, 201, 201, 201, 201, 142, 142, 59, 7, 7, 7, 7, 1, 1, 1, 1, 7, 23, 59, 59, 59, 59, 142, 181, 181, 201, 201, 59, 59, 7, 7, 1, 1, 1, 1, 1, 7] 201 rigid atoms, others: [42, 43, 44, 45, 46, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47]) total number of confs: 605 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114150 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 32, 32, 32, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 32, 65, 153, 153, 153, 153, 153, 201, 201, 153, 65, 32, 32, 32, 32, 7, 4, 4, 2, 2, 32, 32, 153, 153, 201, 201, 201, 201, 201, 153] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 509 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114150 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 21, 31, 31, 31, 31, 31, 10, 10, 1, 6, 20, 20, 20, 20, 20, 59, 59, 20, 6, 1, 1, 1, 1, 10, 21, 21, 31, 31, 1, 1, 20, 20, 59, 59, 59, 59, 59, 20] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114150 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 20, 20, 20, 94, 94, 94, 131, 155, 155, 155, 155, 155, 94, 94, 20, 1, 1, 1, 1, 1, 1, 7, 7, 1, 5, 20, 20, 20, 20, 94, 131, 131, 155, 155, 20, 20, 1, 1, 7, 7, 7, 7, 7, 1] 201 rigid atoms, others: [1, 40, 41, 47, 19, 20, 21, 22, 23, 24, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46]) total number of confs: 498 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114150 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114150/1 /scratch/stefan/7770410/working/building/REAL300020114150 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1918) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1918 `/scratch/stefan/7770410/working/3D/1918' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NC(C2CC2)=C1) `REAL300020114150.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114150/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114150 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 10, 10, 10, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 10, 30, 96, 96, 96, 96, 96, 144, 144, 96, 30, 10, 10, 10, 10, 1, 5, 5, 7, 7, 10, 10, 96, 96, 144, 144, 144, 144, 144, 96] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 380 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114150 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 7, 23, 23, 59, 59, 59, 144, 144, 144, 184, 201, 201, 201, 201, 201, 144, 144, 59, 7, 7, 7, 7, 1, 1, 1, 1, 7, 23, 59, 59, 59, 59, 144, 184, 184, 201, 201, 59, 59, 7, 7, 1, 1, 1, 1, 1, 7] 201 rigid atoms, others: [42, 43, 44, 45, 46, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47]) total number of confs: 596 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114150 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 32, 32, 32, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 32, 65, 153, 153, 153, 153, 153, 201, 201, 153, 65, 32, 32, 32, 32, 7, 4, 4, 2, 2, 32, 32, 153, 153, 201, 201, 201, 201, 201, 153] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 509 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114150 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 21, 30, 30, 30, 30, 30, 10, 10, 1, 6, 20, 20, 20, 20, 20, 59, 59, 20, 6, 1, 1, 1, 1, 10, 21, 21, 30, 30, 1, 1, 20, 20, 59, 59, 59, 59, 59, 20] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114150 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 20, 20, 20, 96, 96, 96, 134, 156, 156, 156, 156, 156, 96, 96, 20, 1, 1, 1, 1, 1, 1, 7, 7, 1, 5, 20, 20, 20, 20, 96, 134, 134, 156, 156, 20, 20, 1, 1, 7, 7, 7, 7, 7, 1] 201 rigid atoms, others: [1, 40, 41, 47, 19, 20, 21, 22, 23, 24, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46]) total number of confs: 494 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114150 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114150 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114150/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114150/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114150 Building REAL300020114151 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114151' /scratch/stefan/7770410/working/building/REAL300020114151 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114151 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114151/0 /scratch/stefan/7770410/working/building/REAL300020114151 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1919) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1919 `/scratch/stefan/7770410/working/3D/1919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CSC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020114151.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114151 none COCC1=CSC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 73, 20, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 26, 33, 42, 42, 42, 42, 6, 6, 1, 20, 97, 97, 97, 73, 73, 20, 6, 1, 1, 1, 1, 6, 26, 26, 33, 33, 1, 1, 20] 201 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45]) total number of confs: 424 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114151 none COCC1=CSC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 110, 34, 34, 34, 34, 14, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 8, 10, 15, 15, 15, 15, 1, 1, 6, 34, 128, 128, 128, 110, 110, 34, 14, 6, 6, 6, 6, 1, 8, 8, 10, 10, 6, 6, 34] 201 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 456 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114151 none COCC1=CSC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 20, 20, 20, 34, 34, 34, 97, 108, 124, 124, 124, 124, 34, 34, 20, 1, 23, 23, 23, 7, 7, 1, 7, 20, 20, 20, 20, 34, 97, 97, 108, 108, 20, 20, 1] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 45, 26] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 482 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114151 none COCC1=CSC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 127, 127, 127, 127, 80, 80, 80, 56, 56, 56, 25, 25, 25, 7, 4, 1, 1, 1, 1, 1, 1, 25, 25, 56, 127, 201, 201, 201, 201, 201, 127, 80, 56, 56, 56, 56, 25, 7, 7, 4, 4, 56, 56, 127] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 702 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114151 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114151/1 /scratch/stefan/7770410/working/building/REAL300020114151 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1920) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1920 `/scratch/stefan/7770410/working/3D/1920' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CSC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020114151.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114151/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114151 none COCC1=CSC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 73, 20, 20, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 26, 33, 42, 42, 42, 42, 6, 6, 1, 20, 97, 97, 97, 73, 73, 20, 6, 1, 1, 1, 1, 6, 26, 26, 33, 33, 1, 1, 20] 201 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 44, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45]) total number of confs: 424 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114151 none COCC1=CSC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 110, 34, 34, 34, 34, 14, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 8, 10, 15, 15, 15, 15, 1, 1, 6, 34, 128, 128, 128, 110, 110, 34, 14, 6, 6, 6, 6, 1, 8, 8, 10, 10, 6, 6, 34] 201 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 456 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114151 none COCC1=CSC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 20, 20, 20, 34, 34, 34, 96, 107, 124, 124, 124, 124, 34, 34, 20, 1, 23, 23, 23, 7, 7, 1, 7, 20, 20, 20, 20, 34, 96, 96, 107, 107, 20, 20, 1] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 45, 26] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 481 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114151 none COCC1=CSC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 127, 127, 127, 127, 80, 80, 80, 56, 56, 56, 25, 25, 25, 7, 4, 1, 1, 1, 1, 1, 1, 25, 25, 56, 127, 201, 201, 201, 201, 201, 127, 80, 56, 56, 56, 56, 25, 7, 7, 4, 4, 56, 56, 127] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 705 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114151 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114151 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114151/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114151/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114151 Building REAL300020114152 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114152' /scratch/stefan/7770410/working/building/REAL300020114152 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114152 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114152/0 /scratch/stefan/7770410/working/building/REAL300020114152 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1921) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1921 `/scratch/stefan/7770410/working/3D/1921' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1) `REAL300020114152.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114152 none CC(C)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 12, 17, 12, 12, 12, 12, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 48, 66, 75, 75, 75, 75, 13, 13, 1, 12, 17, 17, 17, 17, 17, 17, 17, 12, 12, 12, 6, 1, 1, 1, 1, 13, 48, 48, 66, 66, 1, 1] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 327 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114152 none CC(C)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 72, 91, 72, 72, 72, 72, 53, 53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 13, 72, 91, 91, 91, 91, 91, 91, 91, 72, 72, 72, 53, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 321 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114152 none CC(C)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 12, 12, 12, 72, 72, 72, 160, 195, 201, 201, 201, 201, 72, 72, 12, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 12, 12, 12, 12, 72, 160, 160, 195, 195, 12, 12] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 35, 36, 27, 37] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 750 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114152 none CC(C)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 185, 185, 185, 76, 76, 76, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 76, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 185, 76, 76, 76, 76, 13, 6, 6, 4, 4, 76, 76] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 541 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114152 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114152/1 /scratch/stefan/7770410/working/building/REAL300020114152 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1922) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1922 `/scratch/stefan/7770410/working/3D/1922' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1) `REAL300020114152.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114152 none CC(C)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 12, 17, 12, 12, 12, 12, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 48, 66, 75, 75, 75, 75, 13, 13, 1, 12, 17, 17, 17, 17, 17, 17, 17, 12, 12, 12, 6, 1, 1, 1, 1, 13, 48, 48, 66, 66, 1, 1] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 327 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114152 none CC(C)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 72, 91, 72, 72, 72, 72, 53, 53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 13, 72, 91, 91, 91, 91, 91, 91, 91, 72, 72, 72, 53, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 321 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114152 none CC(C)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 12, 12, 12, 72, 72, 72, 160, 195, 201, 201, 201, 201, 72, 72, 12, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 12, 12, 12, 12, 72, 160, 160, 195, 195, 12, 12] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 35, 36, 27, 37] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 750 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114152 none CC(C)C1=CC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 185, 185, 185, 75, 75, 75, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 75, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 185, 75, 75, 75, 75, 12, 6, 6, 4, 4, 75, 75] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 542 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114152 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114152 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114152/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114152/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114152 Building REAL300020114153 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114153' /scratch/stefan/7770410/working/building/REAL300020114153 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114153 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114153/0 /scratch/stefan/7770410/working/building/REAL300020114153 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1923) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1923 `/scratch/stefan/7770410/working/3D/1923' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(N)=O)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114153.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114153 none CN1C=C(C(N)=O)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 11, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 12, 12, 11, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 16, 24, 24, 24, 24, 24, 6, 6, 1, 11, 11, 11, 11, 12, 12, 11, 6, 1, 1, 1, 1, 6, 16, 16, 24, 24, 1, 1] 30 rigid atoms, others: [45, 36, 37, 38, 39, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 122 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114153 none CN1C=C(C(N)=O)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 11, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 15, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 7, 9, 9, 9, 9, 9, 1, 1, 6, 21, 21, 21, 21, 21, 21, 21, 15, 6, 6, 6, 6, 1, 7, 7, 9, 9, 6, 6] 30 rigid atoms, others: [40, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 84 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114153 none CN1C=C(C(N)=O)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 11, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 5, 11, 11, 11, 21, 21, 21, 28, 30, 30, 30, 30, 30, 21, 21, 11, 2, 2, 2, 1, 2, 2, 1, 5, 11, 11, 11, 11, 21, 28, 28, 30, 30, 11, 11] 30 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 34, 31] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 105 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114153 none CN1C=C(C(N)=O)C=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 11, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 29, 28, 28, 28, 25, 25, 25, 12, 12, 12, 5, 2, 1, 1, 1, 1, 1, 1, 12, 12, 25, 29, 29, 29, 29, 29, 29, 29, 28, 25, 25, 25, 25, 12, 5, 5, 2, 2, 25, 25] 29 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 82 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114153 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114153/1 /scratch/stefan/7770410/working/building/REAL300020114153 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1924) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1924 `/scratch/stefan/7770410/working/3D/1924' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(N)=O)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114153.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114153 none CN1C=C(C(N)=O)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 11, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 12, 12, 11, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 16, 24, 24, 24, 24, 24, 6, 6, 1, 11, 11, 11, 11, 12, 12, 11, 6, 1, 1, 1, 1, 6, 16, 16, 24, 24, 1, 1] 30 rigid atoms, others: [45, 36, 37, 38, 39, 11, 12, 13, 14, 15, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 122 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114153 none CN1C=C(C(N)=O)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 11, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 15, 15, 15, 6, 6, 6, 1, 1, 1, 1, 1, 7, 9, 9, 9, 9, 9, 1, 1, 6, 21, 21, 21, 21, 21, 21, 21, 15, 6, 6, 6, 6, 1, 7, 7, 9, 9, 6, 6] 30 rigid atoms, others: [40, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 84 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114153 none CN1C=C(C(N)=O)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 11, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 5, 11, 11, 11, 21, 21, 21, 28, 30, 30, 30, 30, 30, 21, 21, 11, 2, 2, 2, 1, 2, 2, 1, 5, 11, 11, 11, 11, 21, 28, 28, 30, 30, 11, 11] 30 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 34, 31] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 105 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114153 none CN1C=C(C(N)=O)C=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 11, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 29, 28, 28, 28, 25, 25, 25, 12, 12, 12, 5, 2, 1, 1, 1, 1, 1, 1, 12, 12, 25, 29, 29, 29, 29, 29, 29, 29, 28, 25, 25, 25, 25, 12, 5, 5, 2, 2, 25, 25] 29 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 82 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114153 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114153 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114153/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114153/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114153 Building REAL300020114154 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114154' /scratch/stefan/7770410/working/building/REAL300020114154 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114154 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114154/0 /scratch/stefan/7770410/working/building/REAL300020114154 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1925) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1925 `/scratch/stefan/7770410/working/3D/1925' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCOCC1) `REAL300020114154.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114154 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 43, 85, 43, 43, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 85, 85, 85, 85, 85, 85, 85, 85, 85, 85, 85, 85, 43, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 85, 85, 85, 85, 85, 85, 85, 85, 85] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 373 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114154 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 98, 165, 98, 98, 65, 65, 65, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 65, 165, 201, 201, 201, 201, 201, 165, 165, 165, 165, 165, 165, 98, 65, 65, 65, 65, 12, 6, 6, 4, 4, 65, 65, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 756 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114154 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 37, 53, 60, 60, 60, 60, 11, 11, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 11, 37, 37, 53, 53, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 44, 45, 21, 38, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114154 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 5, 5, 5, 15, 15, 15, 85, 85, 85, 159, 201, 201, 201, 201, 201, 85, 85, 15, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 5, 15, 15, 15, 15, 85, 159, 159, 201, 201, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 54, 46, 47, 48, 49, 50, 51, 52, 53, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 768 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114154 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114154/1 /scratch/stefan/7770410/working/building/REAL300020114154 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1926) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1926 `/scratch/stefan/7770410/working/3D/1926' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCOCC1) `REAL300020114154.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114154/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114154 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 43, 85, 43, 43, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 85, 85, 85, 85, 85, 85, 85, 85, 85, 85, 85, 85, 43, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 85, 85, 85, 85, 85, 85, 85, 85, 85] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 370 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114154 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 99, 165, 99, 99, 67, 67, 67, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 67, 165, 201, 201, 201, 201, 201, 165, 165, 165, 165, 165, 165, 99, 67, 67, 67, 67, 12, 6, 6, 4, 4, 67, 67, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 750 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114154 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 36, 52, 60, 60, 60, 60, 11, 11, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 11, 36, 36, 52, 52, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 44, 45, 21, 38, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114154 none CC(C)(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 5, 5, 5, 15, 15, 15, 85, 85, 85, 159, 201, 201, 201, 201, 201, 85, 85, 15, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 5, 15, 15, 15, 15, 85, 159, 159, 201, 201, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 54, 46, 47, 48, 49, 50, 51, 52, 53, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 768 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114154 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114154 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114154/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114154/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114154 Building REAL300020114155 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114155' /scratch/stefan/7770410/working/building/REAL300020114155 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114155 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114155/0 /scratch/stefan/7770410/working/building/REAL300020114155 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1927) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1927 `/scratch/stefan/7770410/working/3D/1927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=C(C=N1)CCCC2) `REAL300020114155.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114155 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=C(C=N1)CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 13, 58, 85, 85, 85, 85, 85, 85, 85, 85, 85, 58, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13, 85, 85, 85, 85, 85, 85, 85, 85, 85, 85] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 234 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114155 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=C(C=N1)CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 90, 90, 90, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 90, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 90, 90, 90, 90, 13, 6, 6, 4, 4, 90, 90, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 557 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114155 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=C(C=N1)CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 54, 76, 89, 89, 89, 89, 13, 13, 1, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 13, 54, 54, 76, 76, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 355 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114155 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC2=C(C=N1)CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 13, 13, 13, 85, 85, 85, 169, 201, 201, 201, 201, 201, 85, 85, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 13, 13, 13, 13, 85, 169, 169, 201, 201, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 715 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114155 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114155/1 /scratch/stefan/7770410/working/building/REAL300020114155 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1928) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1928 `/scratch/stefan/7770410/working/3D/1928' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=C(C=N1)CCCC2) `REAL300020114155.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114155 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=C(C=N1)CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 13, 58, 85, 85, 85, 85, 85, 85, 85, 85, 85, 58, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13, 85, 85, 85, 85, 85, 85, 85, 85, 85, 85] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 234 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114155 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=C(C=N1)CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 90, 90, 90, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 90, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 90, 90, 90, 90, 13, 6, 6, 4, 4, 90, 90, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 557 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114155 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=C(C=N1)CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 54, 76, 89, 89, 89, 89, 13, 13, 1, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 13, 54, 54, 76, 76, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 355 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114155 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC2=C(C=N1)CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 13, 13, 13, 85, 85, 85, 169, 201, 201, 201, 201, 201, 85, 85, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 13, 13, 13, 13, 85, 169, 169, 201, 201, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 715 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114155 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114155 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114155/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114155/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114155 Building REAL300020114156 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114156' /scratch/stefan/7770410/working/building/REAL300020114156 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114156 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114156/0 /scratch/stefan/7770410/working/building/REAL300020114156 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1929) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1929 `/scratch/stefan/7770410/working/3D/1929' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCCC(=O)N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114156.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114156 none O=C(CC1CCCC(=O)N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 1, 11, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 25, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 11, 11, 11, 30, 44, 48, 48, 48, 48, 11, 11, 1, 25, 25, 40, 40, 40, 40, 40, 40, 40, 40, 6, 1, 1, 1, 1, 11, 30, 30, 44, 44, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 320 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114156 none O=C(CC1CCCC(=O)N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 1, 11, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 92, 108, 108, 108, 108, 108, 108, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 92, 92, 108, 108, 108, 108, 108, 108, 108, 108, 28, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 420 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114156 none O=C(CC1CCCC(=O)N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 1, 11, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 5, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 40, 40, 40, 108, 108, 108, 163, 201, 201, 201, 201, 201, 108, 108, 40, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 20, 40, 40, 40, 40, 108, 163, 163, 201, 201, 40, 40] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 36, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 728 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114156 none O=C(CC1CCCC(=O)N1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 1, 11, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 191, 201, 201, 201, 201, 201, 201, 47, 47, 47, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 47, 191, 191, 201, 201, 201, 201, 201, 201, 201, 201, 93, 47, 47, 47, 47, 10, 5, 5, 3, 3, 47, 47] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 755 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114156 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114156/1 /scratch/stefan/7770410/working/building/REAL300020114156 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1930) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1930 `/scratch/stefan/7770410/working/3D/1930' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCCC(=O)N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114156.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114156/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114156 none O=C(CC1CCCC(=O)N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 1, 11, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 25, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 11, 11, 11, 30, 44, 48, 48, 48, 48, 11, 11, 1, 25, 25, 40, 40, 40, 40, 40, 40, 40, 40, 6, 1, 1, 1, 1, 11, 30, 30, 44, 44, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 320 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114156 none O=C(CC1CCCC(=O)N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 1, 11, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 92, 108, 108, 108, 108, 108, 108, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 92, 92, 108, 108, 108, 108, 108, 108, 108, 108, 28, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 420 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114156 none O=C(CC1CCCC(=O)N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 1, 11, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 5, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 40, 40, 40, 108, 108, 108, 163, 201, 201, 201, 201, 201, 108, 108, 40, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 20, 40, 40, 40, 40, 108, 163, 163, 201, 201, 40, 40] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 36, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 728 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114156 none O=C(CC1CCCC(=O)N1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 1, 11, 8, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 191, 201, 201, 201, 201, 201, 201, 46, 46, 46, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 46, 191, 191, 201, 201, 201, 201, 201, 201, 201, 201, 92, 46, 46, 46, 46, 9, 5, 5, 3, 3, 46, 46] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 751 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114156 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114156 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114156/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114156/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114156 Building REAL300020114157 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114157' /scratch/stefan/7770410/working/building/REAL300020114157 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114157 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114157/0 /scratch/stefan/7770410/working/building/REAL300020114157 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1931) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1931 `/scratch/stefan/7770410/working/3D/1931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1) `REAL300020114157.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114157 none NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 13, 15, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 50, 67, 79, 79, 79, 79, 12, 12, 1, 13, 15, 15, 13, 13, 6, 1, 1, 1, 1, 12, 50, 50, 67, 67, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40]) total number of confs: 316 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114157 none NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 71, 76, 71, 71, 71, 46, 46, 46, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 12, 71, 76, 76, 71, 71, 46, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12] 201 rigid atoms, others: [36, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 223 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114157 none NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 71, 71, 71, 143, 191, 191, 191, 191, 191, 71, 71, 13, 1, 3, 3, 1, 1, 4, 13, 13, 13, 13, 71, 143, 143, 191, 191, 13, 13] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 26, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 758 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114157 none NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 191, 201, 191, 191, 191, 156, 156, 156, 81, 81, 81, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 81, 191, 201, 201, 191, 191, 156, 81, 81, 81, 81, 18, 6, 6, 4, 4, 81, 81] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 543 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114157 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114157/1 /scratch/stefan/7770410/working/building/REAL300020114157 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1932) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1932 `/scratch/stefan/7770410/working/3D/1932' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1) `REAL300020114157.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114157 none NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 13, 15, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 49, 66, 80, 80, 80, 80, 12, 12, 1, 13, 15, 15, 13, 13, 6, 1, 1, 1, 1, 12, 49, 49, 66, 66, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40]) total number of confs: 317 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114157 none NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 72, 77, 72, 72, 72, 46, 46, 46, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 12, 72, 77, 77, 72, 72, 46, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12] 201 rigid atoms, others: [36, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 225 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114157 none NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 72, 72, 72, 144, 192, 192, 192, 192, 192, 72, 72, 13, 1, 3, 3, 1, 1, 4, 13, 13, 13, 13, 72, 144, 144, 192, 192, 13, 13] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 26, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 756 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114157 none NC(=O)C1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 191, 201, 191, 191, 191, 156, 156, 156, 81, 81, 81, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 81, 191, 201, 201, 191, 191, 156, 81, 81, 81, 81, 17, 6, 6, 4, 4, 81, 81] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 544 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114157 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114157 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114157/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114157/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114157 Building REAL300020114158 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114158' /scratch/stefan/7770410/working/building/REAL300020114158 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114158 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114158/0 /scratch/stefan/7770410/working/building/REAL300020114158 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1933) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1933 `/scratch/stefan/7770410/working/3D/1933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=CC(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020114158.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114158 none COC1=CN=CC(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 47, 47, 47, 47, 47, 32, 28, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 18, 28, 28, 28, 28, 28, 8, 8, 1, 47, 54, 54, 54, 47, 47, 32, 32, 28, 28, 6, 1, 1, 1, 1, 8, 18, 18, 28, 28, 1, 1, 47] 201 rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 14, 15, 48, 49, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50]) total number of confs: 278 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114158 none COC1=CN=CC(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [135, 134, 134, 134, 134, 134, 97, 83, 25, 25, 25, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 134, 135, 135, 135, 134, 134, 97, 97, 83, 83, 25, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8, 134] 201 rigid atoms, others: [43, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 487 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114158 none COC1=CN=CC(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 2, 4, 21, 21, 21, 47, 47, 47, 134, 134, 134, 166, 201, 201, 201, 201, 201, 134, 134, 47, 1, 3, 3, 3, 1, 1, 2, 2, 4, 4, 21, 47, 47, 47, 47, 134, 166, 166, 201, 201, 47, 47, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 50, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 670 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114158 none COC1=CN=CC(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 155, 140, 71, 71, 71, 32, 32, 32, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 32, 201, 201, 201, 201, 201, 201, 155, 155, 140, 140, 71, 32, 32, 32, 32, 7, 4, 4, 2, 2, 32, 32, 201] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 685 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114158 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114158/1 /scratch/stefan/7770410/working/building/REAL300020114158 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1934) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1934 `/scratch/stefan/7770410/working/3D/1934' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=CC(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020114158.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114158 none COC1=CN=CC(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 46, 46, 46, 46, 46, 32, 28, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 19, 29, 29, 29, 29, 29, 8, 8, 1, 46, 53, 53, 53, 46, 46, 32, 32, 28, 28, 6, 1, 1, 1, 1, 8, 19, 19, 29, 29, 1, 1, 46] 201 rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 14, 15, 48, 49, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50]) total number of confs: 279 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114158 none COC1=CN=CC(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 132, 132, 132, 132, 132, 95, 81, 25, 25, 25, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 132, 133, 133, 133, 132, 132, 95, 95, 81, 81, 25, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8, 132] 201 rigid atoms, others: [43, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 481 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114158 none COC1=CN=CC(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 2, 4, 21, 21, 21, 46, 46, 46, 132, 132, 132, 165, 201, 201, 201, 201, 201, 132, 132, 46, 1, 3, 3, 3, 1, 1, 2, 2, 4, 4, 21, 46, 46, 46, 46, 132, 165, 165, 201, 201, 46, 46, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 50, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 674 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114158 none COC1=CN=CC(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 157, 142, 72, 72, 72, 32, 32, 32, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 32, 201, 201, 201, 201, 201, 201, 157, 157, 142, 142, 72, 32, 32, 32, 32, 7, 4, 4, 2, 2, 32, 32, 201] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 686 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114158 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114158 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114158/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114158/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114158 Building REAL300020114159 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114159' /scratch/stefan/7770410/working/building/REAL300020114159 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114159 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114159/0 /scratch/stefan/7770410/working/building/REAL300020114159 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1935) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1935 `/scratch/stefan/7770410/working/3D/1935' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C)=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1C) `REAL300020114159.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114159 none CC1=NC(C)=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 41, 59, 65, 65, 65, 65, 13, 13, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 13, 41, 41, 59, 59, 1, 1, 13, 13, 13] 201 rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 11, 12, 45, 44, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 272 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114159 none CC1=NC(C)=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 103, 103, 58, 58, 58, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 103, 103, 103, 103, 103, 103, 103, 103, 103, 58, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 103, 103, 103] 201 rigid atoms, others: [39, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 261 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114159 none CC1=NC(C)=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 103, 103, 103, 172, 201, 201, 201, 201, 201, 103, 103, 13, 1, 1, 1, 2, 2, 2, 2, 2, 2, 5, 13, 13, 13, 13, 103, 172, 172, 201, 201, 13, 13, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 682 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114159 none CC1=NC(C)=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 169, 169, 169, 65, 65, 65, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 65, 201, 201, 201, 201, 201, 201, 201, 201, 201, 169, 65, 65, 65, 65, 10, 6, 6, 4, 4, 65, 65, 201, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 527 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114159 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114159/1 /scratch/stefan/7770410/working/building/REAL300020114159 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1936) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1936 `/scratch/stefan/7770410/working/3D/1936' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C)=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1C) `REAL300020114159.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114159 none CC1=NC(C)=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 40, 58, 64, 64, 64, 64, 13, 13, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 13, 40, 40, 58, 58, 1, 1, 13, 13, 13] 201 rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 11, 12, 45, 44, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 269 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114159 none CC1=NC(C)=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 103, 103, 58, 58, 58, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 103, 103, 103, 103, 103, 103, 103, 103, 103, 58, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13, 103, 103, 103] 201 rigid atoms, others: [39, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 261 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114159 none CC1=NC(C)=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 103, 103, 103, 172, 201, 201, 201, 201, 201, 103, 103, 13, 1, 1, 1, 2, 2, 2, 2, 2, 2, 5, 13, 13, 13, 13, 103, 172, 172, 201, 201, 13, 13, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 685 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114159 none CC1=NC(C)=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 172, 172, 172, 66, 66, 66, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 66, 201, 201, 201, 201, 201, 201, 201, 201, 201, 172, 66, 66, 66, 66, 12, 6, 6, 4, 4, 66, 66, 201, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 528 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114159 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114159 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114159/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114159/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114159 Building REAL300020114160 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114160' /scratch/stefan/7770410/working/building/REAL300020114160 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114160 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114160/0 /scratch/stefan/7770410/working/building/REAL300020114160 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1937) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1937 `/scratch/stefan/7770410/working/3D/1937' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1Cl) `REAL300020114160.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114160 none CN1N=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 7, 7, 7, 1, 1, 1, 1, 1, 13, 13, 13, 51, 71, 85, 85, 85, 85, 13, 13, 1, 19, 19, 19, 19, 19, 19, 7, 1, 1, 1, 1, 13, 51, 51, 71, 71, 1, 1, 19] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 39, 40, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41]) total number of confs: 339 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114160 none CN1N=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 48, 48, 48, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 17, 17, 17, 17, 1, 1, 13, 92, 92, 92, 92, 92, 92, 48, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 92] 201 rigid atoms, others: [34, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 241 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114160 none CN1N=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 92, 92, 92, 155, 201, 201, 201, 201, 201, 92, 92, 19, 1, 1, 1, 2, 2, 2, 6, 19, 19, 19, 19, 92, 155, 155, 201, 201, 19, 19, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 41, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 731 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114160 none CN1N=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 155, 155, 155, 87, 87, 87, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 87, 201, 201, 201, 201, 201, 201, 155, 87, 87, 87, 87, 17, 6, 6, 4, 4, 87, 87, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 501 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114160 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114160/1 /scratch/stefan/7770410/working/building/REAL300020114160 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1938) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1938 `/scratch/stefan/7770410/working/3D/1938' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1Cl) `REAL300020114160.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114160/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114160 none CN1N=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 7, 7, 7, 1, 1, 1, 1, 1, 13, 13, 13, 51, 71, 85, 85, 85, 85, 13, 13, 1, 19, 19, 19, 19, 19, 19, 7, 1, 1, 1, 1, 13, 51, 51, 71, 71, 1, 1, 19] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 39, 40, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41]) total number of confs: 339 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114160 none CN1N=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 48, 48, 48, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 17, 17, 17, 17, 1, 1, 13, 92, 92, 92, 92, 92, 92, 48, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 92] 201 rigid atoms, others: [34, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 241 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114160 none CN1N=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 92, 92, 92, 155, 201, 201, 201, 201, 201, 92, 92, 19, 1, 1, 1, 2, 2, 2, 6, 19, 19, 19, 19, 92, 155, 155, 201, 201, 19, 19, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 41, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 731 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114160 none CN1N=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 154, 154, 154, 88, 88, 88, 18, 18, 18, 7, 4, 1, 1, 1, 1, 1, 1, 18, 18, 88, 201, 201, 201, 201, 201, 201, 154, 88, 88, 88, 88, 18, 7, 7, 4, 4, 88, 88, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 501 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114160 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114160 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114160/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114160/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114160 Building REAL300020114161 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114161' /scratch/stefan/7770410/working/building/REAL300020114161 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114161 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114161/0 /scratch/stefan/7770410/working/building/REAL300020114161 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1939) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1939 `/scratch/stefan/7770410/working/3D/1939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(F)=C1) `REAL300020114161.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114161 none CC1=CC(F)=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 44, 60, 76, 76, 76, 76, 11, 11, 1, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 44, 44, 60, 60, 1, 1, 22] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 385 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114161 none CC1=CC(F)=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 38, 107, 107, 107, 38, 38, 38, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 14, 14, 14, 14, 1, 1, 11, 107, 107, 107, 107, 107, 107, 107, 38, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 107] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 640 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114161 none CC1=CC(F)=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 23, 23, 108, 108, 108, 166, 201, 201, 201, 201, 201, 108, 108, 23, 1, 1, 1, 2, 2, 2, 1, 7, 23, 23, 23, 23, 108, 166, 166, 201, 201, 23, 23, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 44, 25, 26, 27, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 706 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114161 none CC1=CC(F)=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 164, 201, 201, 201, 153, 153, 153, 78, 78, 78, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 78, 201, 201, 201, 201, 201, 201, 201, 153, 78, 78, 78, 78, 15, 6, 6, 4, 4, 78, 78, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 687 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114161 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114161/1 /scratch/stefan/7770410/working/building/REAL300020114161 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1940) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1940 `/scratch/stefan/7770410/working/3D/1940' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(F)=C1) `REAL300020114161.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114161 none CC1=CC(F)=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 22, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 44, 60, 76, 76, 76, 76, 11, 11, 1, 22, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 44, 44, 60, 60, 1, 1, 22] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 385 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114161 none CC1=CC(F)=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 38, 107, 107, 107, 38, 38, 38, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 14, 14, 14, 14, 1, 1, 11, 107, 107, 107, 107, 107, 107, 107, 38, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 107] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 638 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114161 none CC1=CC(F)=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 23, 23, 108, 108, 108, 166, 201, 201, 201, 201, 201, 108, 108, 23, 1, 1, 1, 2, 2, 2, 1, 7, 23, 23, 23, 23, 108, 166, 166, 201, 201, 23, 23, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 44, 25, 26, 27, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 706 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114161 none CC1=CC(F)=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 165, 201, 201, 201, 154, 154, 154, 78, 78, 78, 16, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 78, 201, 201, 201, 201, 201, 201, 201, 154, 78, 78, 78, 78, 16, 6, 6, 4, 4, 78, 78, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 693 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114161 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114161 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114161/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114161/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114161 Building REAL300020114162 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114162' /scratch/stefan/7770410/working/building/REAL300020114162 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114162 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114162/0 /scratch/stefan/7770410/working/building/REAL300020114162 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1941) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1941 `/scratch/stefan/7770410/working/3D/1941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114162.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114162 none CCCC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 14, 14, 14, 14, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 22, 35, 35, 35, 35, 35, 8, 8, 1, 24, 24, 24, 24, 24, 24, 24, 14, 14, 14, 14, 5, 1, 1, 1, 1, 8, 22, 22, 35, 35, 1, 1] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 230 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114162 none CCCC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 54, 54, 54, 54, 54, 54, 21, 21, 21, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 101, 101, 101, 101, 101, 101, 101, 54, 54, 54, 54, 21, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 418 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114162 none CCCC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 54, 54, 54, 86, 109, 109, 109, 109, 109, 54, 54, 14, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 14, 14, 14, 14, 54, 86, 86, 109, 109, 14, 14] 201 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 3, 36, 38, 37] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 408 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114162 none CCCC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 109, 109, 109, 109, 109, 109, 65, 65, 65, 36, 36, 36, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 36, 201, 201, 201, 201, 201, 201, 201, 109, 109, 109, 109, 65, 36, 36, 36, 36, 8, 4, 4, 2, 2, 36, 36] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 815 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114162 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114162/1 /scratch/stefan/7770410/working/building/REAL300020114162 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1942) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1942 `/scratch/stefan/7770410/working/3D/1942' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114162.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114162 none CCCC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 14, 14, 14, 14, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 22, 35, 35, 35, 35, 35, 8, 8, 1, 24, 24, 24, 24, 24, 24, 24, 14, 14, 14, 14, 5, 1, 1, 1, 1, 8, 22, 22, 35, 35, 1, 1] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 49, 50, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 230 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114162 none CCCC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 54, 54, 54, 54, 54, 54, 21, 21, 21, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 101, 101, 101, 101, 101, 101, 101, 54, 54, 54, 54, 21, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [44, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 418 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114162 none CCCC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 54, 54, 54, 86, 109, 109, 109, 109, 109, 54, 54, 14, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 14, 14, 14, 14, 54, 86, 86, 109, 109, 14, 14] 201 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 3, 36, 38, 37] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 408 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114162 none CCCC1=CC=CC=C1C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 109, 109, 109, 109, 109, 109, 65, 65, 65, 36, 36, 36, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 36, 201, 201, 201, 201, 201, 201, 201, 109, 109, 109, 109, 65, 36, 36, 36, 36, 8, 4, 4, 2, 2, 36, 36] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 815 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114162 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114162 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114162/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114162/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114162 Building REAL300020114163 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114163' /scratch/stefan/7770410/working/building/REAL300020114163 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114163 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114163/0 /scratch/stefan/7770410/working/building/REAL300020114163 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1943) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1943 `/scratch/stefan/7770410/working/3D/1943' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1) `REAL300020114163.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114163 none COC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 15, 11, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 56, 73, 89, 89, 89, 89, 11, 11, 1, 15, 16, 24, 24, 24, 16, 6, 1, 1, 1, 1, 11, 56, 56, 73, 73, 1, 1, 16] 201 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43]) total number of confs: 380 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114163 none COC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 76, 71, 80, 80, 47, 47, 47, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 11, 80, 80, 109, 109, 109, 80, 47, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 80] 201 rigid atoms, others: [36, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 323 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114163 none COC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 16, 16, 16, 80, 80, 80, 160, 186, 201, 201, 201, 201, 80, 80, 16, 1, 1, 3, 3, 3, 1, 4, 16, 16, 16, 16, 80, 160, 160, 186, 186, 16, 16, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 43, 25, 26, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 663 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114163 none COC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 91, 91, 91, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 91, 201, 201, 201, 201, 201, 201, 201, 91, 91, 91, 91, 17, 6, 6, 4, 4, 91, 91, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 541 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114163 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114163/1 /scratch/stefan/7770410/working/building/REAL300020114163 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1944) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1944 `/scratch/stefan/7770410/working/3D/1944' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1) `REAL300020114163.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114163 none COC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 15, 11, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 57, 74, 90, 90, 90, 90, 11, 11, 1, 15, 16, 24, 24, 24, 16, 6, 1, 1, 1, 1, 11, 57, 57, 74, 74, 1, 1, 16] 201 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43]) total number of confs: 383 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114163 none COC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 76, 71, 80, 80, 47, 47, 47, 11, 11, 11, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 11, 80, 80, 109, 109, 109, 80, 47, 11, 11, 11, 11, 1, 9, 9, 11, 11, 11, 11, 80] 201 rigid atoms, others: [36, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 323 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114163 none COC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 16, 16, 16, 80, 80, 80, 161, 186, 201, 201, 201, 201, 80, 80, 16, 1, 1, 3, 3, 3, 1, 4, 16, 16, 16, 16, 80, 161, 161, 186, 186, 16, 16, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 43, 25, 26, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 663 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114163 none COC1=CN=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 92, 92, 92, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 92, 201, 201, 201, 201, 201, 201, 201, 92, 92, 92, 92, 18, 6, 6, 4, 4, 92, 92, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 540 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114163 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114163 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114163/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114163/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114163 Building REAL300020114164 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114164' /scratch/stefan/7770410/working/building/REAL300020114164 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114164 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114164/0 /scratch/stefan/7770410/working/building/REAL300020114164 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1945) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1945 `/scratch/stefan/7770410/working/3D/1945' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1C) `REAL300020114164.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114164 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 56, 74, 96, 96, 96, 96, 12, 12, 1, 13, 13, 13, 41, 41, 41, 13, 6, 1, 1, 1, 1, 12, 56, 56, 74, 74, 1, 1, 13, 13, 13] 201 rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 388 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114164 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 69, 69, 69, 50, 50, 50, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 12, 69, 69, 69, 108, 108, 108, 69, 50, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 69, 69, 69] 201 rigid atoms, others: [36, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 273 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114164 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 69, 69, 69, 145, 190, 201, 201, 201, 201, 69, 69, 13, 1, 1, 1, 8, 8, 8, 1, 4, 13, 13, 13, 13, 69, 145, 145, 190, 190, 13, 13, 2, 2, 2] 201 rigid atoms, others: [1, 2, 3, 4, 5, 24, 25, 26, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 756 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114164 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 194, 194, 194, 95, 95, 95, 16, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 95, 201, 201, 201, 201, 201, 201, 201, 194, 95, 95, 95, 95, 16, 6, 6, 4, 4, 95, 95, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 551 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114164 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114164/1 /scratch/stefan/7770410/working/building/REAL300020114164 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1946) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1946 `/scratch/stefan/7770410/working/3D/1946' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1C) `REAL300020114164.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114164 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 56, 74, 96, 96, 96, 96, 12, 12, 1, 13, 13, 13, 41, 41, 41, 13, 6, 1, 1, 1, 1, 12, 56, 56, 74, 74, 1, 1, 13, 13, 13] 201 rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 388 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114164 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 69, 69, 69, 50, 50, 50, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 12, 69, 69, 69, 108, 108, 108, 69, 50, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 69, 69, 69] 201 rigid atoms, others: [36, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 273 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114164 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 69, 69, 69, 145, 190, 201, 201, 201, 201, 69, 69, 13, 1, 1, 1, 8, 8, 8, 1, 4, 13, 13, 13, 13, 69, 145, 145, 190, 190, 13, 13, 2, 2, 2] 201 rigid atoms, others: [1, 2, 3, 4, 5, 24, 25, 26, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 756 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114164 none COC1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 195, 195, 195, 96, 96, 96, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 96, 201, 201, 201, 201, 201, 201, 201, 195, 96, 96, 96, 96, 17, 6, 6, 4, 4, 96, 96, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 550 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114164 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114164 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114164/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114164/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114164 Building REAL300020114165 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114165' /scratch/stefan/7770410/working/building/REAL300020114165 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114165 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114165/0 /scratch/stefan/7770410/working/building/REAL300020114165 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1947) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1947 `/scratch/stefan/7770410/working/3D/1947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN=C1C(F)F) `REAL300020114165.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114165 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN=C1C(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 35, 100, 100, 100, 100, 100, 100, 110, 110, 35, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 100, 100, 100, 110] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 276 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114165 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN=C1C(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 52, 52, 52, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 52, 114, 201, 201, 201, 201, 201, 201, 201, 201, 114, 52, 52, 52, 52, 11, 6, 6, 4, 4, 52, 52, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 466 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114165 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN=C1C(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 48, 54, 54, 54, 54, 11, 11, 1, 6, 20, 20, 20, 20, 20, 20, 30, 30, 6, 1, 1, 1, 1, 11, 33, 33, 48, 48, 1, 1, 20, 20, 20, 30] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 294 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114165 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CN=C1C(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 20, 20, 20, 100, 100, 100, 167, 201, 201, 201, 201, 201, 100, 100, 20, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 20, 20, 20, 20, 100, 167, 167, 201, 201, 20, 20, 1, 1, 1, 6] 201 rigid atoms, others: [1, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43]) total number of confs: 728 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114165 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114165/1 /scratch/stefan/7770410/working/building/REAL300020114165 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1948) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1948 `/scratch/stefan/7770410/working/3D/1948' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN=C1C(F)F) `REAL300020114165.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114165 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN=C1C(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 35, 100, 100, 100, 100, 100, 100, 110, 110, 35, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 100, 100, 100, 110] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 276 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114165 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN=C1C(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 51, 51, 51, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 51, 113, 201, 201, 201, 201, 201, 201, 201, 201, 113, 51, 51, 51, 51, 10, 6, 6, 4, 4, 51, 51, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 466 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114165 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN=C1C(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 48, 54, 54, 54, 54, 11, 11, 1, 6, 21, 21, 21, 21, 21, 21, 31, 31, 6, 1, 1, 1, 1, 11, 33, 33, 48, 48, 1, 1, 21, 21, 21, 31] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 295 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114165 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CN=C1C(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 8, 1, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 21, 21, 21, 100, 100, 100, 167, 201, 201, 201, 201, 201, 100, 100, 21, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 21, 21, 21, 21, 100, 167, 167, 201, 201, 21, 21, 1, 1, 1, 6] 201 rigid atoms, others: [1, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43]) total number of confs: 731 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114165 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114165 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114165/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114165/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114165 Building REAL300020114166 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114166' /scratch/stefan/7770410/working/building/REAL300020114166 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114166 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114166/0 /scratch/stefan/7770410/working/building/REAL300020114166 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1949) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1949 `/scratch/stefan/7770410/working/3D/1949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=CC(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020114166.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114166 none CC1=CN=CC(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 35, 35, 24, 22, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 19, 30, 30, 30, 30, 30, 7, 7, 1, 35, 35, 35, 35, 35, 35, 24, 24, 22, 22, 5, 1, 1, 1, 1, 7, 19, 19, 30, 30, 1, 1, 35] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49]) total number of confs: 235 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114166 none CC1=CN=CC(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [121, 121, 121, 121, 121, 80, 68, 21, 21, 21, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 121, 121, 121, 121, 121, 121, 80, 80, 68, 68, 21, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 121] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 422 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114166 none CC1=CN=CC(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 4, 17, 17, 17, 35, 35, 35, 121, 121, 121, 157, 201, 201, 201, 201, 201, 121, 121, 35, 1, 2, 2, 2, 1, 1, 2, 2, 4, 4, 17, 35, 35, 35, 35, 121, 157, 157, 201, 201, 35, 35, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 49, 27, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 695 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114166 none CC1=CN=CC(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 136, 121, 55, 55, 55, 32, 32, 32, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 32, 201, 201, 201, 201, 201, 201, 136, 136, 121, 121, 55, 32, 32, 32, 32, 9, 4, 4, 2, 2, 32, 32, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 666 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114166 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114166/1 /scratch/stefan/7770410/working/building/REAL300020114166 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1950) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1950 `/scratch/stefan/7770410/working/3D/1950' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=CC(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020114166.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114166/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114166 none CC1=CN=CC(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 35, 35, 24, 22, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 19, 30, 30, 30, 30, 30, 7, 7, 1, 35, 35, 35, 35, 35, 35, 24, 24, 22, 22, 5, 1, 1, 1, 1, 7, 19, 19, 30, 30, 1, 1, 35] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 49]) total number of confs: 235 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114166 none CC1=CN=CC(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 119, 119, 119, 79, 67, 21, 21, 21, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 119, 119, 119, 119, 119, 119, 79, 79, 67, 67, 21, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7, 119] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 417 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114166 none CC1=CN=CC(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 4, 17, 17, 17, 35, 35, 35, 119, 119, 119, 156, 201, 201, 201, 201, 201, 119, 119, 35, 1, 2, 2, 2, 1, 1, 2, 2, 4, 4, 17, 35, 35, 35, 35, 119, 156, 156, 201, 201, 35, 35, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 49, 27, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 705 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114166 none CC1=CN=CC(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 137, 122, 56, 56, 56, 32, 32, 32, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 32, 201, 201, 201, 201, 201, 201, 137, 137, 122, 122, 56, 32, 32, 32, 32, 9, 4, 4, 2, 2, 32, 32, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 666 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114166 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114166 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114166/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114166/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114166 Building REAL300020114167 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114167' /scratch/stefan/7770410/working/building/REAL300020114167 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114167 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114167/0 /scratch/stefan/7770410/working/building/REAL300020114167 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1951) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1951 `/scratch/stefan/7770410/working/3D/1951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCCC1) `REAL300020114167.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114167 none CC1(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 17, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 17, 20, 20, 20, 20, 20, 13, 13, 1, 43, 43, 43, 43, 43, 43, 43, 43, 17, 17, 6, 1, 1, 1, 1, 13, 17, 17, 20, 20, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 42, 43, 21] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 194 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114167 none CC1(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [191, 83, 45, 45, 45, 13, 13, 13, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 1, 1, 13, 191, 191, 191, 191, 191, 191, 191, 191, 83, 83, 45, 13, 13, 13, 13, 1, 3, 3, 5, 5, 13, 13, 191, 191, 191, 191, 191, 191, 191, 191, 191, 191] 201 rigid atoms, others: [37, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 680 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114167 none CC1(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 8, 16, 16, 16, 43, 43, 43, 191, 191, 191, 195, 201, 201, 201, 201, 201, 191, 191, 43, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 16, 43, 43, 43, 43, 191, 195, 195, 201, 201, 43, 43, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 22, 23, 24, 25, 26] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 371 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114167 none CC1(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 93, 59, 59, 59, 25, 25, 25, 6, 6, 6, 5, 2, 1, 1, 1, 1, 1, 1, 6, 6, 25, 201, 201, 201, 201, 201, 201, 201, 201, 93, 93, 59, 25, 25, 25, 25, 6, 5, 5, 2, 2, 25, 25, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 712 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114167 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114167/1 /scratch/stefan/7770410/working/building/REAL300020114167 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1952) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1952 `/scratch/stefan/7770410/working/3D/1952' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCCC1) `REAL300020114167.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114167 none CC1(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 18, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 17, 20, 20, 20, 20, 20, 13, 13, 1, 44, 44, 44, 44, 44, 44, 44, 44, 18, 18, 6, 1, 1, 1, 1, 13, 17, 17, 20, 20, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 42, 43, 21] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 197 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114167 none CC1(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [192, 84, 45, 45, 45, 13, 13, 13, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 1, 1, 13, 192, 192, 192, 192, 192, 192, 192, 192, 84, 84, 45, 13, 13, 13, 13, 1, 3, 3, 5, 5, 13, 13, 192, 192, 192, 192, 192, 192, 192, 192, 192, 192] 201 rigid atoms, others: [37, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 683 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114167 none CC1(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 8, 16, 16, 16, 44, 44, 44, 192, 192, 192, 195, 201, 201, 201, 201, 201, 192, 192, 44, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 16, 44, 44, 44, 44, 192, 195, 195, 201, 201, 44, 44, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 22, 23, 24, 25, 26] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 367 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114167 none CC1(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 93, 59, 59, 59, 25, 25, 25, 6, 6, 6, 5, 2, 1, 1, 1, 1, 1, 1, 6, 6, 25, 201, 201, 201, 201, 201, 201, 201, 201, 93, 93, 59, 25, 25, 25, 25, 6, 5, 5, 2, 2, 25, 25, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 712 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114167 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114167 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114167/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114167/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114167 Building REAL300020114168 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114168' /scratch/stefan/7770410/working/building/REAL300020114168 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114168 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114168/0 /scratch/stefan/7770410/working/building/REAL300020114168 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1953) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1953 `/scratch/stefan/7770410/working/3D/1953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCC1) `REAL300020114168.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114168 none CC(C)CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 39, 55, 60, 60, 60, 60, 10, 10, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 10, 39, 39, 55, 55, 1, 1, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 46, 47, 40, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50, 51, 52, 53]) total number of confs: 263 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114168 none CC(C)CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 76, 44, 44, 44, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 11, 11, 11, 11, 1, 1, 10, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 44, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 76, 76, 76, 76, 76, 76] 201 rigid atoms, others: [41, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 271 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114168 none CC(C)CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 1, 1, 1, 3, 3, 3, 11, 11, 11, 76, 76, 76, 169, 201, 201, 201, 201, 201, 76, 76, 11, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 11, 11, 11, 11, 76, 169, 169, 201, 201, 11, 11, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 48, 49, 50, 51, 52, 53, 24, 25, 26] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 771 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114168 none CC(C)CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 146, 146, 119, 119, 119, 65, 65, 65, 15, 15, 15, 8, 4, 1, 1, 1, 1, 1, 1, 15, 15, 65, 146, 146, 146, 146, 146, 146, 146, 146, 146, 146, 146, 146, 119, 65, 65, 65, 65, 15, 8, 8, 4, 4, 65, 65, 146, 146, 146, 146, 146, 146] 146 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 444 number of broken/clashed sets: 143 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114168 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114168/1 /scratch/stefan/7770410/working/building/REAL300020114168 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1954) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1954 `/scratch/stefan/7770410/working/3D/1954' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC1) `REAL300020114168.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114168/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114168 none CC(C)CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 39, 55, 60, 60, 60, 60, 10, 10, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 10, 39, 39, 55, 55, 1, 1, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 46, 47, 40, 23] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50, 51, 52, 53]) total number of confs: 263 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114168 none CC(C)CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 76, 44, 44, 44, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 11, 11, 11, 11, 1, 1, 10, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 44, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 76, 76, 76, 76, 76, 76] 201 rigid atoms, others: [41, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 271 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114168 none CC(C)CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 1, 1, 1, 3, 3, 3, 11, 11, 11, 76, 76, 76, 167, 201, 201, 201, 201, 201, 76, 76, 11, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 11, 11, 11, 11, 76, 167, 167, 201, 201, 11, 11, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 48, 49, 50, 51, 52, 53, 24, 25, 26] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 774 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114168 none CC(C)CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 146, 146, 119, 119, 119, 65, 65, 65, 15, 15, 15, 8, 4, 1, 1, 1, 1, 1, 1, 15, 15, 65, 146, 146, 146, 146, 146, 146, 146, 146, 146, 146, 146, 146, 119, 65, 65, 65, 65, 15, 8, 8, 4, 4, 65, 65, 146, 146, 146, 146, 146, 146] 146 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 444 number of broken/clashed sets: 143 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114168 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114168 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114168/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114168/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114168 Building REAL300020114169 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114169' /scratch/stefan/7770410/working/building/REAL300020114169 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114169 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114169/0 /scratch/stefan/7770410/working/building/REAL300020114169 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1955) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1955 `/scratch/stefan/7770410/working/3D/1955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC2=CN=CC=C2S1) `REAL300020114169.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114169 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC2=CN=CC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 8, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 13, 59, 95, 95, 95, 95, 95, 95, 95, 95, 59, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13, 95, 95, 95] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 257 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114169 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC2=CN=CC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 8, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 82, 82, 82, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 82, 189, 201, 201, 201, 201, 201, 201, 201, 201, 189, 82, 82, 82, 82, 14, 6, 6, 4, 4, 82, 82, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 539 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114169 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC2=CN=CC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 8, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 50, 71, 82, 82, 82, 82, 13, 13, 1, 6, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 13, 50, 50, 71, 71, 1, 1, 19, 19, 19] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 339 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114169 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NC2=CN=CC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 8, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 19, 19, 19, 95, 95, 95, 172, 201, 201, 201, 201, 201, 95, 95, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 19, 19, 19, 19, 95, 172, 172, 201, 201, 19, 19, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 681 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114169 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114169/1 /scratch/stefan/7770410/working/building/REAL300020114169 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1956) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1956 `/scratch/stefan/7770410/working/3D/1956' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC2=CN=CC=C2S1) `REAL300020114169.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114169/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114169 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC2=CN=CC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 8, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 13, 59, 96, 96, 96, 96, 96, 96, 96, 96, 59, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13, 96, 96, 96] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 259 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114169 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC2=CN=CC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 8, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 83, 83, 83, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 83, 189, 201, 201, 201, 201, 201, 201, 201, 201, 189, 83, 83, 83, 83, 15, 6, 6, 4, 4, 83, 83, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 538 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114169 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC2=CN=CC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 8, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 50, 71, 82, 82, 82, 82, 13, 13, 1, 6, 19, 19, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 13, 50, 50, 71, 71, 1, 1, 19, 19, 19] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 339 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114169 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NC2=CN=CC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 1, 1, 8, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 19, 19, 19, 96, 96, 96, 172, 201, 201, 201, 201, 201, 96, 96, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 19, 19, 19, 19, 96, 172, 172, 201, 201, 19, 19, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 679 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114169 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114169 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114169/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114169/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114169 Building REAL300020114170 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114170' /scratch/stefan/7770410/working/building/REAL300020114170 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114170 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114170/0 /scratch/stefan/7770410/working/building/REAL300020114170 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1957) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1957 `/scratch/stefan/7770410/working/3D/1957' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCCCCC1) `REAL300020114170.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114170 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 35, 98, 98, 98, 98, 98, 98, 98, 35, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 307 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114170 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 57, 57, 57, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 57, 112, 201, 201, 201, 201, 201, 201, 201, 112, 57, 57, 57, 57, 11, 6, 6, 4, 4, 57, 57, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 601 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114170 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 49, 55, 55, 55, 55, 11, 11, 1, 6, 29, 29, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 11, 33, 33, 49, 49, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 278 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114170 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 29, 29, 29, 98, 98, 98, 176, 201, 201, 201, 201, 201, 98, 98, 29, 1, 1, 1, 1, 1, 1, 1, 1, 8, 29, 29, 29, 29, 98, 176, 176, 201, 201, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 678 number of broken/clashed sets: 201 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114170 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114170/1 /scratch/stefan/7770410/working/building/REAL300020114170 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1958) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1958 `/scratch/stefan/7770410/working/3D/1958' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCCCCC1) `REAL300020114170.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114170 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 36, 98, 98, 98, 98, 98, 98, 98, 36, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 305 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114170 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 55, 55, 55, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 55, 110, 201, 201, 201, 201, 201, 201, 201, 110, 55, 55, 55, 55, 10, 6, 6, 4, 4, 55, 55, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 605 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114170 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 48, 55, 55, 55, 55, 11, 11, 1, 6, 29, 29, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 11, 33, 33, 48, 48, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 274 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114170 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 29, 29, 29, 98, 98, 98, 176, 201, 201, 201, 201, 201, 98, 98, 29, 1, 1, 1, 1, 1, 1, 1, 1, 8, 29, 29, 29, 29, 98, 176, 176, 201, 201, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 19, 20, 21, 22, 23, 24, 25, 26, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 678 number of broken/clashed sets: 201 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114170 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114170 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114170/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114170/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114170 Building REAL300020114171 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114171' /scratch/stefan/7770410/working/building/REAL300020114171 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114171 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114171/0 /scratch/stefan/7770410/working/building/REAL300020114171 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1959) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1959 `/scratch/stefan/7770410/working/3D/1959' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(C2=CC=CO2)O1) `REAL300020114171.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114171 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(C2=CC=CO2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 17, 17, 17, 17, 1, 1, 7, 27, 60, 60, 60, 60, 102, 102, 102, 102, 60, 27, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7, 60, 60, 102, 102, 102] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 232 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114171 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(C2=CC=CO2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 8, 22, 22, 50, 50, 50, 102, 102, 102, 179, 201, 201, 201, 201, 201, 102, 102, 50, 8, 8, 8, 1, 1, 1, 1, 1, 1, 8, 22, 50, 50, 50, 50, 102, 179, 179, 201, 201, 50, 50, 8, 8, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 718 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114171 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(C2=CC=CO2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [144, 144, 75, 75, 75, 24, 24, 24, 7, 4, 1, 1, 1, 1, 1, 1, 24, 24, 75, 144, 186, 186, 186, 186, 201, 201, 201, 201, 186, 144, 75, 75, 75, 75, 24, 7, 7, 4, 4, 75, 75, 186, 186, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 507 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114171 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(C2=CC=CO2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 41, 51, 67, 67, 67, 67, 7, 7, 1, 6, 23, 23, 23, 23, 50, 50, 50, 50, 23, 6, 1, 1, 1, 1, 7, 41, 41, 51, 51, 1, 1, 23, 23, 50, 50, 50] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114171 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C(C2=CC=CO2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 23, 23, 23, 60, 60, 60, 148, 173, 181, 181, 181, 181, 60, 60, 23, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 7, 23, 23, 23, 23, 60, 148, 148, 173, 173, 23, 23, 1, 1, 8, 8, 8] 201 rigid atoms, others: [1, 41, 42, 19, 20, 21, 22, 23, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 672 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114171 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114171/1 /scratch/stefan/7770410/working/building/REAL300020114171 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1960) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1960 `/scratch/stefan/7770410/working/3D/1960' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(C2=CC=CO2)O1) `REAL300020114171.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2', 'output.5.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114171 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(C2=CC=CO2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 7, 7, 7, 1, 1, 1, 1, 1, 9, 11, 17, 17, 17, 17, 1, 1, 7, 27, 60, 60, 60, 60, 102, 102, 102, 102, 60, 27, 7, 7, 7, 7, 1, 9, 9, 11, 11, 7, 7, 60, 60, 102, 102, 102] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 232 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.5.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.5.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114171 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(C2=CC=CO2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 8, 22, 22, 50, 50, 50, 102, 102, 102, 179, 201, 201, 201, 201, 201, 102, 102, 50, 8, 8, 8, 1, 1, 1, 1, 1, 1, 8, 22, 50, 50, 50, 50, 102, 179, 179, 201, 201, 50, 50, 8, 8, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 716 number of broken/clashed sets: 0 ./output.5.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114171 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(C2=CC=CO2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [145, 145, 75, 75, 75, 24, 24, 24, 7, 4, 1, 1, 1, 1, 1, 1, 24, 24, 75, 145, 187, 187, 187, 187, 201, 201, 201, 201, 187, 145, 75, 75, 75, 75, 24, 7, 7, 4, 4, 75, 75, 187, 187, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 507 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114171 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(C2=CC=CO2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 40, 50, 66, 66, 66, 66, 7, 7, 1, 6, 23, 23, 23, 23, 50, 50, 50, 50, 23, 6, 1, 1, 1, 1, 7, 40, 40, 50, 50, 1, 1, 23, 23, 50, 50, 50] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 287 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114171 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C(C2=CC=CO2)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 23, 23, 23, 60, 60, 60, 148, 174, 182, 182, 182, 182, 60, 60, 23, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 7, 23, 23, 23, 23, 60, 148, 148, 174, 174, 23, 23, 1, 1, 8, 8, 8] 201 rigid atoms, others: [1, 41, 42, 19, 20, 21, 22, 23, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 678 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114171 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114171 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114171/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114171/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114171 Building REAL300020114172 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114172' /scratch/stefan/7770410/working/building/REAL300020114172 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114172 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114172/0 /scratch/stefan/7770410/working/building/REAL300020114172 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1961) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1961 `/scratch/stefan/7770410/working/3D/1961' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1) `REAL300020114172.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114172 none COCCN1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 29, 25, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 35, 48, 49, 49, 49, 49, 11, 11, 1, 6, 34, 34, 34, 29, 29, 25, 25, 6, 6, 6, 1, 1, 1, 1, 11, 35, 35, 48, 48, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 309 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114172 none COCCN1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 134, 126, 42, 42, 42, 42, 42, 42, 42, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 42, 139, 139, 139, 134, 134, 126, 126, 42, 42, 42, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 559 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114172 none COCCN1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 8, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 42, 42, 42, 107, 136, 137, 137, 137, 137, 42, 42, 6, 1, 12, 12, 12, 8, 8, 6, 6, 1, 1, 2, 6, 6, 6, 6, 42, 107, 107, 136, 136, 6, 6] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 3, 36, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 564 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114172 none COCCN1C=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 198, 141, 141, 141, 141, 141, 141, 141, 49, 49, 49, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 49, 141, 201, 201, 201, 201, 201, 198, 198, 141, 141, 141, 49, 49, 49, 49, 9, 5, 5, 3, 3, 49, 49] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 740 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114172 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114172/1 /scratch/stefan/7770410/working/building/REAL300020114172 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1962) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1962 `/scratch/stefan/7770410/working/3D/1962' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1) `REAL300020114172.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114172/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114172 none COCCN1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 29, 25, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 35, 48, 49, 49, 49, 49, 11, 11, 1, 6, 34, 34, 34, 29, 29, 25, 25, 6, 6, 6, 1, 1, 1, 1, 11, 35, 35, 48, 48, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 309 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114172 none COCCN1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 134, 126, 42, 42, 42, 42, 42, 42, 42, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 11, 42, 139, 139, 139, 134, 134, 126, 126, 42, 42, 42, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 559 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114172 none COCCN1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 8, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 42, 42, 42, 107, 136, 137, 137, 137, 137, 42, 42, 6, 1, 12, 12, 12, 8, 8, 6, 6, 1, 1, 2, 6, 6, 6, 6, 42, 107, 107, 136, 136, 6, 6] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 3, 36, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 564 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114172 none COCCN1C=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 198, 140, 140, 140, 140, 140, 140, 140, 49, 49, 49, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 49, 140, 201, 201, 201, 201, 201, 198, 198, 140, 140, 140, 49, 49, 49, 49, 9, 5, 5, 3, 3, 49, 49] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 742 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114172 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114172 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114172/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114172/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114172 Building REAL300020114173 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114173' /scratch/stefan/7770410/working/building/REAL300020114173 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114173 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114173/0 /scratch/stefan/7770410/working/building/REAL300020114173 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1963) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1963 `/scratch/stefan/7770410/working/3D/1963' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=CC(=O)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020114173.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114173 none CN1C=CC(=O)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 35, 35, 35, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 26, 36, 42, 42, 42, 42, 6, 6, 1, 35, 35, 35, 35, 35, 35, 6, 1, 1, 1, 1, 6, 26, 26, 36, 36, 1, 1, 35] 111 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 199 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114173 none CN1C=CC(=O)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 63, 63, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 8, 12, 15, 15, 15, 15, 1, 1, 6, 63, 63, 63, 63, 63, 63, 19, 6, 6, 6, 6, 1, 8, 8, 12, 12, 6, 6, 63] 111 rigid atoms, others: [37, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 161 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114173 none CN1C=CC(=O)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 35, 35, 35, 63, 63, 63, 99, 111, 111, 111, 111, 111, 63, 63, 35, 1, 2, 2, 2, 1, 1, 12, 35, 35, 35, 35, 63, 99, 99, 111, 111, 35, 35, 1] 111 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 26, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 408 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114173 none CN1C=CC(=O)C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 113, 113, 113, 79, 79, 79, 47, 47, 47, 20, 20, 20, 7, 4, 1, 1, 1, 1, 1, 1, 20, 20, 47, 113, 113, 113, 113, 113, 113, 79, 47, 47, 47, 47, 20, 7, 7, 4, 4, 47, 47, 113] 113 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 293 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114173 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114173/1 /scratch/stefan/7770410/working/building/REAL300020114173 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1964) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1964 `/scratch/stefan/7770410/working/3D/1964' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=CC(=O)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020114173.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114173 none CN1C=CC(=O)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 35, 35, 35, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 26, 36, 41, 41, 41, 41, 6, 6, 1, 35, 35, 35, 35, 35, 35, 6, 1, 1, 1, 1, 6, 26, 26, 36, 36, 1, 1, 35] 109 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44]) total number of confs: 197 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114173 none CN1C=CC(=O)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 62, 62, 62, 19, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 8, 12, 15, 15, 15, 15, 1, 1, 6, 62, 62, 62, 62, 62, 62, 19, 6, 6, 6, 6, 1, 8, 8, 12, 12, 6, 6, 62] 109 rigid atoms, others: [37, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 160 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114173 none CN1C=CC(=O)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 35, 35, 35, 62, 62, 62, 97, 109, 109, 109, 109, 109, 62, 62, 35, 1, 2, 2, 2, 1, 1, 12, 35, 35, 35, 35, 62, 97, 97, 109, 109, 35, 35, 1] 109 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 26, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 400 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114173 none CN1C=CC(=O)C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 109, 109, 109, 109, 75, 75, 75, 45, 45, 45, 19, 19, 19, 7, 4, 1, 1, 1, 1, 1, 1, 19, 19, 45, 109, 109, 109, 109, 109, 109, 75, 45, 45, 45, 45, 19, 7, 7, 4, 4, 45, 45, 109] 109 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 282 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114173 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114173 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114173/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114173/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114173 Building REAL300020114174 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114174' /scratch/stefan/7770410/working/building/REAL300020114174 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114174 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114174/0 /scratch/stefan/7770410/working/building/REAL300020114174 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1965) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1965 `/scratch/stefan/7770410/working/3D/1965' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=C(COCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1) `REAL300020114174.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114174 none CC1=CN=C(COCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 94, 45, 21, 17, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 20, 31, 31, 31, 31, 31, 7, 7, 1, 94, 94, 94, 94, 94, 45, 45, 17, 17, 5, 1, 1, 1, 1, 7, 20, 20, 31, 31, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 375 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114174 none CC1=CN=C(COCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [155, 155, 155, 155, 91, 46, 42, 17, 17, 17, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 155, 155, 155, 155, 155, 91, 91, 42, 42, 17, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 510 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114174 none CC1=CN=C(COCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 28, 46, 59, 59, 59, 94, 94, 94, 155, 155, 155, 191, 201, 201, 201, 201, 201, 155, 155, 94, 1, 2, 2, 2, 1, 9, 9, 46, 46, 59, 94, 94, 94, 94, 155, 191, 191, 201, 201, 94, 94] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 700 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114174 none CC1=CN=C(COCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 126, 61, 58, 26, 26, 26, 22, 22, 22, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 22, 201, 201, 201, 201, 201, 126, 126, 58, 58, 26, 22, 22, 22, 22, 7, 4, 4, 2, 2, 22, 22] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 642 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114174 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114174/1 /scratch/stefan/7770410/working/building/REAL300020114174 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1966) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1966 `/scratch/stefan/7770410/working/3D/1966' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=C(COCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1) `REAL300020114174.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114174 none CC1=CN=C(COCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 95, 46, 21, 17, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 20, 31, 31, 31, 31, 31, 7, 7, 1, 95, 95, 95, 95, 95, 46, 46, 17, 17, 5, 1, 1, 1, 1, 7, 20, 20, 31, 31, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 378 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114174 none CC1=CN=C(COCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [155, 155, 155, 155, 92, 46, 42, 17, 17, 17, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 155, 155, 155, 155, 155, 92, 92, 42, 42, 17, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 511 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114174 none CC1=CN=C(COCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 28, 46, 60, 60, 60, 95, 95, 95, 155, 155, 155, 191, 201, 201, 201, 201, 201, 155, 155, 95, 1, 2, 2, 2, 1, 9, 9, 46, 46, 60, 95, 95, 95, 95, 155, 191, 191, 201, 201, 95, 95] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 703 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114174 none CC1=CN=C(COCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 126, 60, 58, 25, 25, 25, 21, 21, 21, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 21, 201, 201, 201, 201, 201, 126, 126, 58, 58, 25, 21, 21, 21, 21, 7, 4, 4, 2, 2, 21, 21] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 648 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114174 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114174 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114174/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114174/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114174 Building REAL300020114175 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114175' /scratch/stefan/7770410/working/building/REAL300020114175 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114175 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114175/0 /scratch/stefan/7770410/working/building/REAL300020114175 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1967) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1967 `/scratch/stefan/7770410/working/3D/1967' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NC2=NNN=C21) `REAL300020114175.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114175 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NC2=NNN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 13, 13, 13, 1, 1, 1, 1, 1, 9, 12, 20, 20, 20, 20, 1, 1, 13, 51, 84, 84, 84, 84, 84, 84, 84, 84, 51, 13, 13, 13, 13, 1, 9, 9, 12, 12, 13, 13, 84, 84, 84] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 245 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114175 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NC2=NNN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [197, 197, 110, 110, 110, 25, 25, 25, 6, 4, 1, 1, 1, 1, 1, 1, 25, 25, 110, 197, 201, 201, 201, 201, 201, 201, 201, 201, 197, 110, 110, 110, 110, 25, 6, 6, 4, 4, 110, 110, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 542 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114175 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NC2=NNN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 70, 90, 110, 110, 110, 110, 13, 13, 1, 6, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 13, 70, 70, 90, 90, 1, 1, 15, 15, 15] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 404 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114175 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=NC2=NNN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 15, 15, 15, 84, 84, 84, 176, 201, 201, 201, 201, 201, 84, 84, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 15, 84, 176, 176, 201, 201, 15, 15, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 708 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114175 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114175/1 /scratch/stefan/7770410/working/building/REAL300020114175 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1968) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1968 `/scratch/stefan/7770410/working/3D/1968' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NC2=NNN=C21) `REAL300020114175.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114175 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NC2=NNN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 21, 21, 21, 21, 1, 1, 13, 50, 83, 83, 83, 83, 83, 83, 83, 83, 50, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 83, 83, 83] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 249 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114175 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NC2=NNN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [198, 198, 113, 113, 113, 26, 26, 26, 6, 4, 1, 1, 1, 1, 1, 1, 26, 26, 113, 198, 201, 201, 201, 201, 201, 201, 201, 201, 198, 113, 113, 113, 113, 26, 6, 6, 4, 4, 113, 113, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 538 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114175 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NC2=NNN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 70, 91, 112, 112, 112, 112, 13, 13, 1, 6, 14, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 13, 70, 70, 91, 91, 1, 1, 14, 14, 14] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 411 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114175 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=NC2=NNN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 8, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 14, 14, 14, 83, 83, 83, 176, 201, 201, 201, 201, 201, 83, 83, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 14, 14, 14, 14, 83, 176, 176, 201, 201, 14, 14, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 708 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114175 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114175 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114175/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114175/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114175 Building REAL300020114176 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114176' /scratch/stefan/7770410/working/building/REAL300020114176 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114176 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114176/0 /scratch/stefan/7770410/working/building/REAL300020114176 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1969) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1969 `/scratch/stefan/7770410/working/3D/1969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C(Cl)S1) `REAL300020114176.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114176 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C(Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 16, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 36, 54, 63, 63, 63, 63, 13, 13, 1, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 13, 36, 36, 54, 54, 1, 1] 201 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 39, 40, 21, 30, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38]) total number of confs: 268 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114176 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C(Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 16, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 53, 53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 108, 108, 108, 108, 108, 108, 108, 53, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [34, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 261 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114176 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C(Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 16, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 18, 18, 18, 108, 108, 108, 170, 201, 201, 201, 201, 201, 108, 108, 18, 1, 1, 1, 1, 2, 2, 2, 7, 18, 18, 18, 18, 108, 170, 170, 201, 201, 18, 18] 201 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 659 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114176 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)N=C(Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 16, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 165, 165, 165, 63, 63, 63, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 63, 201, 201, 201, 201, 201, 201, 201, 165, 63, 63, 63, 63, 10, 6, 6, 4, 4, 63, 63] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 529 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114176 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114176/1 /scratch/stefan/7770410/working/building/REAL300020114176 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1970) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1970 `/scratch/stefan/7770410/working/3D/1970' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C(Cl)S1) `REAL300020114176.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114176 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C(Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 16, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 37, 55, 63, 63, 63, 63, 13, 13, 1, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 13, 37, 37, 55, 55, 1, 1] 201 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 39, 40, 21, 30, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38]) total number of confs: 269 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114176 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C(Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 16, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 53, 53, 53, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 108, 108, 108, 108, 108, 108, 108, 53, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [34, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 261 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114176 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C(Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 16, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 18, 18, 18, 108, 108, 108, 170, 201, 201, 201, 201, 201, 108, 108, 18, 1, 1, 1, 1, 2, 2, 2, 7, 18, 18, 18, 18, 108, 170, 170, 201, 201, 18, 18] 201 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 659 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114176 none CC1=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)N=C(Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 1, 16, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 166, 166, 166, 63, 63, 63, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 63, 201, 201, 201, 201, 201, 201, 201, 166, 63, 63, 63, 63, 10, 6, 6, 4, 4, 63, 63] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 531 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114176 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114176 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114176/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114176/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114176 Building REAL300020114177 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114177' /scratch/stefan/7770410/working/building/REAL300020114177 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114177 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114177/0 /scratch/stefan/7770410/working/building/REAL300020114177 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1971) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1971 `/scratch/stefan/7770410/working/3D/1971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=CC=CN2C=C1) `REAL300020114177.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114177 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=CC=CN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 8, 8, 8, 1, 1, 1, 1, 1, 9, 13, 17, 17, 17, 17, 1, 1, 8, 27, 93, 93, 93, 93, 93, 93, 93, 93, 27, 8, 8, 8, 8, 1, 9, 9, 13, 13, 8, 8, 93, 93, 93, 93, 93, 93] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 212 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114177 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=CC=CN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [135, 135, 70, 70, 70, 23, 23, 23, 7, 4, 1, 1, 1, 1, 1, 1, 23, 23, 70, 135, 201, 201, 201, 201, 201, 201, 201, 201, 135, 70, 70, 70, 70, 23, 7, 7, 4, 4, 70, 70, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 482 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114177 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=CC=CN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 38, 49, 62, 62, 62, 62, 8, 8, 1, 6, 37, 37, 37, 37, 37, 37, 37, 37, 6, 1, 1, 1, 1, 8, 38, 38, 49, 49, 1, 1, 37, 37, 37, 37, 37, 37] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114177 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=CC=CN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 37, 37, 37, 93, 93, 93, 173, 201, 201, 201, 201, 201, 93, 93, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 37, 37, 37, 37, 93, 173, 173, 201, 201, 37, 37, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 725 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114177 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114177/1 /scratch/stefan/7770410/working/building/REAL300020114177 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1972) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1972 `/scratch/stefan/7770410/working/3D/1972' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=CC=CN2C=C1) `REAL300020114177.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114177 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=CC=CN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 8, 8, 8, 1, 1, 1, 1, 1, 9, 13, 17, 17, 17, 17, 1, 1, 8, 27, 94, 94, 94, 94, 94, 94, 94, 94, 27, 8, 8, 8, 8, 1, 9, 9, 13, 13, 8, 8, 94, 94, 94, 94, 94, 94] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 213 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114177 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=CC=CN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 70, 70, 70, 23, 23, 23, 7, 4, 1, 1, 1, 1, 1, 1, 23, 23, 70, 134, 201, 201, 201, 201, 201, 201, 201, 201, 134, 70, 70, 70, 70, 23, 7, 7, 4, 4, 70, 70, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 480 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114177 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=CC=CN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 38, 49, 62, 62, 62, 62, 8, 8, 1, 6, 37, 37, 37, 37, 37, 37, 37, 37, 6, 1, 1, 1, 1, 8, 38, 38, 49, 49, 1, 1, 37, 37, 37, 37, 37, 37] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114177 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=CC=CN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 37, 37, 37, 94, 94, 94, 172, 201, 201, 201, 201, 201, 94, 94, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 37, 37, 37, 37, 94, 172, 172, 201, 201, 37, 37, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 726 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114177 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114177 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114177/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114177/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114177 Building REAL300020114178 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114178' /scratch/stefan/7770410/working/building/REAL300020114178 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114178 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114178/0 /scratch/stefan/7770410/working/building/REAL300020114178 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1973) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1973 `/scratch/stefan/7770410/working/3D/1973' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=CC=CC2=CN=N1) `REAL300020114178.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114178 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=CC=CC2=CN=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 36, 86, 86, 86, 86, 86, 86, 86, 86, 86, 36, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 86, 86, 86, 86, 86] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 208 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114178 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=CC=CC2=CN=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [140, 140, 71, 71, 71, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 71, 140, 201, 201, 201, 201, 201, 201, 201, 201, 201, 140, 71, 71, 71, 71, 12, 6, 6, 4, 4, 71, 71, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 508 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114178 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=CC=CC2=CN=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 44, 62, 71, 71, 71, 71, 11, 11, 1, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 11, 44, 44, 62, 62, 1, 1, 18, 18, 18, 18, 18] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 295 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114178 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C2C=CC=CC2=CN=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 18, 18, 18, 86, 86, 86, 154, 201, 201, 201, 201, 201, 86, 86, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 18, 18, 18, 18, 86, 154, 154, 201, 201, 18, 18, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 763 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114178 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114178/1 /scratch/stefan/7770410/working/building/REAL300020114178 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1974) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1974 `/scratch/stefan/7770410/working/3D/1974' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=CC=CC2=CN=N1) `REAL300020114178.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114178/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114178 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=CC=CC2=CN=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 11, 11, 11, 1, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 1, 1, 11, 36, 86, 86, 86, 86, 86, 86, 86, 86, 86, 36, 11, 11, 11, 11, 1, 8, 8, 10, 10, 11, 11, 86, 86, 86, 86, 86] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 208 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114178 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=CC=CC2=CN=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [140, 140, 71, 71, 71, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 71, 140, 201, 201, 201, 201, 201, 201, 201, 201, 201, 140, 71, 71, 71, 71, 12, 6, 6, 4, 4, 71, 71, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 510 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114178 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=CC=CC2=CN=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 44, 62, 71, 71, 71, 71, 11, 11, 1, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 11, 44, 44, 62, 62, 1, 1, 18, 18, 18, 18, 18] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 295 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114178 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C2C=CC=CC2=CN=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 18, 18, 18, 86, 86, 86, 154, 201, 201, 201, 201, 201, 86, 86, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 18, 18, 18, 18, 86, 154, 154, 201, 201, 18, 18, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 763 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114178 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114178 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114178/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114178/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114178 Building REAL300020114179 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114179' /scratch/stefan/7770410/working/building/REAL300020114179 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114179 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114179/0 /scratch/stefan/7770410/working/building/REAL300020114179 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1975) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1975 `/scratch/stefan/7770410/working/3D/1975' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC2=CC=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=C12) `REAL300020114179.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114179 none CC1=NNC2=CC=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 28, 42, 43, 43, 43, 43, 9, 9, 1, 14, 14, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 9, 28, 28, 42, 42, 1, 1, 14] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47]) total number of confs: 196 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114179 none CC1=NNC2=CC=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 72, 72, 72, 72, 25, 25, 25, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 9, 72, 72, 72, 72, 72, 72, 72, 72, 25, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 72] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 162 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114179 none CC1=NNC2=CC=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 72, 72, 72, 146, 201, 201, 201, 201, 201, 72, 72, 14, 1, 1, 2, 2, 2, 1, 1, 1, 5, 14, 14, 14, 14, 72, 146, 146, 201, 201, 14, 14, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 34, 47, 33, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 824 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114179 none CC1=NNC2=CC=C(C(=O)NC3CC(N4C=C(CCC5=N[N-]N=N5)N=N4)C3)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 76, 76, 76, 44, 44, 44, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 44, 201, 201, 201, 201, 201, 201, 201, 201, 76, 44, 44, 44, 44, 9, 5, 5, 3, 3, 44, 44, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 401 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114179 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114179/1 /scratch/stefan/7770410/working/building/REAL300020114179 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1976) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1976 `/scratch/stefan/7770410/working/3D/1976' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC2=CC=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=C12) `REAL300020114179.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114179 none CC1=NNC2=CC=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 28, 42, 43, 43, 43, 43, 9, 9, 1, 14, 14, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 9, 28, 28, 42, 42, 1, 1, 14] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 45, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 47]) total number of confs: 196 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114179 none CC1=NNC2=CC=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 72, 72, 72, 72, 25, 25, 25, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 9, 72, 72, 72, 72, 72, 72, 72, 72, 25, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 72] 201 rigid atoms, others: [40, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 162 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114179 none CC1=NNC2=CC=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 72, 72, 72, 146, 201, 201, 201, 201, 201, 72, 72, 14, 1, 1, 2, 2, 2, 1, 1, 1, 5, 14, 14, 14, 14, 72, 146, 146, 201, 201, 14, 14, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 34, 47, 33, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 824 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114179 none CC1=NNC2=CC=C(C(=O)NC3CC(N4C=C(CCC5=NN=N[N-]5)N=N4)C3)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 78, 78, 78, 45, 45, 45, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 45, 201, 201, 201, 201, 201, 201, 201, 201, 78, 45, 45, 45, 45, 11, 6, 6, 4, 4, 45, 45, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 402 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114179 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114179 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114179/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114179/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114179 Building REAL300020114180 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114180' /scratch/stefan/7770410/working/building/REAL300020114180 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114180 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114180/0 /scratch/stefan/7770410/working/building/REAL300020114180 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1977) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1977 `/scratch/stefan/7770410/working/3D/1977' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](OCC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114180.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114180 none C[C@H](OCC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 6, 9, 9, 11, 23, 41, 41, 24, 41, 41, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 25, 37, 37, 37, 37, 37, 8, 8, 1, 9, 9, 9, 23, 23, 41, 41, 41, 41, 41, 6, 1, 1, 1, 1, 8, 25, 25, 37, 37, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 13, 14, 15, 16, 17, 50, 51, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 349 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114180 none C[C@H](OCC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 25, 37, 37, 42, 91, 121, 121, 92, 121, 121, 25, 25, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 37, 37, 37, 91, 91, 121, 121, 121, 121, 121, 25, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [45, 16, 17, 18, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 608 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114180 none C[C@H](OCC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 10, 13, 3, 1, 1, 1, 1, 1, 1, 1, 13, 18, 18, 18, 41, 41, 41, 121, 121, 121, 179, 201, 201, 201, 201, 201, 121, 121, 41, 13, 13, 13, 3, 3, 1, 1, 1, 1, 1, 18, 41, 41, 41, 41, 121, 179, 179, 201, 201, 41, 41] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 39, 36, 38, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 680 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114180 none C[C@H](OCC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 80, 105, 105, 110, 201, 201, 201, 201, 201, 201, 80, 80, 37, 37, 37, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 37, 105, 105, 105, 201, 201, 201, 201, 201, 201, 201, 80, 37, 37, 37, 37, 7, 4, 4, 2, 2, 37, 37] 201 rigid atoms, others: [21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 838 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114180 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114180/1 /scratch/stefan/7770410/working/building/REAL300020114180 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1978) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1978 `/scratch/stefan/7770410/working/3D/1978' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](OCC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114180.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114180 none C[C@H](OCC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 6, 9, 9, 11, 23, 41, 41, 24, 41, 41, 6, 6, 1, 1, 1, 1, 1, 8, 8, 8, 25, 37, 37, 37, 37, 37, 8, 8, 1, 9, 9, 9, 23, 23, 41, 41, 41, 41, 41, 6, 1, 1, 1, 1, 8, 25, 25, 37, 37, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 13, 14, 15, 16, 17, 50, 51, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 349 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114180 none C[C@H](OCC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 25, 37, 37, 42, 91, 120, 120, 92, 120, 120, 25, 25, 8, 8, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 8, 37, 37, 37, 91, 91, 120, 120, 120, 120, 120, 25, 8, 8, 8, 8, 1, 5, 5, 7, 7, 8, 8] 201 rigid atoms, others: [45, 16, 17, 18, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 601 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114180 none C[C@H](OCC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 10, 13, 3, 1, 1, 1, 1, 1, 1, 1, 13, 18, 18, 18, 41, 41, 41, 120, 120, 120, 178, 201, 201, 201, 201, 201, 120, 120, 41, 13, 13, 13, 3, 3, 1, 1, 1, 1, 1, 18, 41, 41, 41, 41, 120, 178, 178, 201, 201, 41, 41] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 39, 36, 38, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 685 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114180 none C[C@H](OCC1=CC=CC=C1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 81, 106, 106, 110, 201, 201, 201, 201, 201, 201, 81, 81, 37, 37, 37, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 37, 106, 106, 106, 201, 201, 201, 201, 201, 201, 201, 81, 37, 37, 37, 37, 7, 4, 4, 2, 2, 37, 37] 201 rigid atoms, others: [21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 838 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114180 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114180 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114180/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114180/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114180 Building REAL300020114181 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114181' /scratch/stefan/7770410/working/building/REAL300020114181 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114181 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114181/0 /scratch/stefan/7770410/working/building/REAL300020114181 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1979) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1979 `/scratch/stefan/7770410/working/3D/1979' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN2CCCOC2=C1) `REAL300020114181.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114181 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN2CCCOC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 13, 58, 86, 86, 86, 86, 86, 86, 86, 86, 58, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13, 86, 86, 86, 86, 86, 86, 86] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 239 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114181 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN2CCCOC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 101, 101, 101, 16, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 101, 200, 201, 201, 201, 201, 201, 201, 201, 201, 200, 101, 101, 101, 101, 16, 6, 6, 4, 4, 101, 101, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 552 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114181 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN2CCCOC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 58, 81, 101, 101, 101, 101, 13, 13, 1, 6, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 13, 58, 58, 81, 81, 1, 1, 15, 15, 15, 15, 15, 15, 15] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 389 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114181 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=NN2CCCOC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 15, 15, 15, 86, 86, 86, 168, 201, 201, 201, 201, 201, 86, 86, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 15, 15, 15, 15, 86, 168, 168, 201, 201, 15, 15, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 724 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114181 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114181/1 /scratch/stefan/7770410/working/building/REAL300020114181 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1980) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1980 `/scratch/stefan/7770410/working/3D/1980' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN2CCCOC2=C1) `REAL300020114181.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114181/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114181 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN2CCCOC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 14, 14, 14, 14, 1, 1, 13, 58, 86, 86, 86, 86, 86, 86, 86, 86, 58, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13, 86, 86, 86, 86, 86, 86, 86] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 239 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114181 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN2CCCOC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 101, 101, 101, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 101, 200, 201, 201, 201, 201, 201, 201, 201, 201, 200, 101, 101, 101, 101, 17, 6, 6, 4, 4, 101, 101, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 551 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114181 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN2CCCOC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 58, 81, 101, 101, 101, 101, 13, 13, 1, 6, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 13, 58, 58, 81, 81, 1, 1, 15, 15, 15, 15, 15, 15, 15] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 18, 38, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 389 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114181 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=NN2CCCOC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 5, 5, 5, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 15, 15, 15, 86, 86, 86, 168, 201, 201, 201, 201, 201, 86, 86, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 15, 15, 15, 15, 86, 168, 168, 201, 201, 15, 15, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 724 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114181 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114181 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114181/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114181/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114181 Building REAL300020114182 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114182' /scratch/stefan/7770410/working/building/REAL300020114182 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114182 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114182/0 /scratch/stefan/7770410/working/building/REAL300020114182 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1981) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1981 `/scratch/stefan/7770410/working/3D/1981' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1) `REAL300020114182.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114182 none COC1=NC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 8, 8, 8, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 39, 57, 61, 61, 61, 61, 13, 13, 1, 8, 13, 13, 13, 8, 8, 6, 1, 1, 1, 1, 13, 39, 39, 57, 57, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 264 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114182 none COC1=NC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 61, 61, 61, 61, 61, 55, 55, 55, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 61, 97, 97, 97, 61, 61, 55, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [37, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 253 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114182 none COC1=NC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 61, 61, 61, 141, 197, 201, 201, 201, 201, 61, 61, 8, 1, 3, 3, 3, 1, 1, 3, 8, 8, 8, 8, 61, 141, 141, 197, 197, 8, 8] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 26, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 792 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114182 none COC1=NC=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 195, 195, 195, 61, 61, 61, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 61, 201, 201, 201, 201, 201, 201, 195, 61, 61, 61, 61, 10, 6, 6, 4, 4, 61, 61] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 523 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114182 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114182/1 /scratch/stefan/7770410/working/building/REAL300020114182 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1982) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1982 `/scratch/stefan/7770410/working/3D/1982' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1) `REAL300020114182.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114182/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114182 none COC1=NC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 8, 8, 8, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 39, 57, 61, 61, 61, 61, 13, 13, 1, 8, 13, 13, 13, 8, 8, 6, 1, 1, 1, 1, 13, 39, 39, 57, 57, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 264 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114182 none COC1=NC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 61, 61, 61, 61, 61, 55, 55, 55, 13, 13, 13, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 13, 61, 96, 96, 96, 61, 61, 55, 13, 13, 13, 13, 1, 6, 6, 8, 8, 13, 13] 201 rigid atoms, others: [37, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 251 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114182 none COC1=NC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 61, 61, 61, 142, 197, 201, 201, 201, 201, 61, 61, 8, 1, 3, 3, 3, 1, 1, 3, 8, 8, 8, 8, 61, 142, 142, 197, 197, 8, 8] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 26, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 792 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114182 none COC1=NC=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 195, 195, 195, 61, 61, 61, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 61, 201, 201, 201, 201, 201, 201, 195, 61, 61, 61, 61, 10, 6, 6, 4, 4, 61, 61] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 523 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114182 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114182 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114182/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114182/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114182 Building REAL300020114183 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114183' /scratch/stefan/7770410/working/building/REAL300020114183 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114183 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114183/0 /scratch/stefan/7770410/working/building/REAL300020114183 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1983) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1983 `/scratch/stefan/7770410/working/3D/1983' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1) `REAL300020114183.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114183 none COC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 40, 40, 24, 19, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 20, 32, 32, 32, 32, 32, 8, 8, 1, 40, 40, 40, 40, 40, 40, 40, 24, 24, 19, 19, 5, 1, 1, 1, 1, 8, 20, 20, 32, 32, 1, 1, 40] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50]) total number of confs: 255 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114183 none COC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 119, 119, 119, 66, 58, 16, 16, 16, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 119, 119, 119, 119, 119, 119, 119, 66, 66, 58, 58, 16, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 119] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 391 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114183 none COC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 7, 23, 23, 23, 40, 40, 40, 119, 119, 119, 161, 201, 201, 201, 201, 201, 119, 119, 40, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 23, 40, 40, 40, 40, 119, 161, 161, 201, 201, 40, 40, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 50, 33, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 717 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114183 none COC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 113, 103, 46, 46, 46, 32, 32, 32, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 32, 201, 201, 201, 201, 201, 201, 201, 113, 113, 103, 103, 46, 32, 32, 32, 32, 8, 4, 4, 2, 2, 32, 32, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 615 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114183 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114183/1 /scratch/stefan/7770410/working/building/REAL300020114183 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1984) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1984 `/scratch/stefan/7770410/working/3D/1984' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1) `REAL300020114183.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114183 none COC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 40, 40, 24, 20, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 20, 32, 32, 32, 32, 32, 8, 8, 1, 40, 40, 40, 40, 40, 40, 40, 24, 24, 20, 20, 5, 1, 1, 1, 1, 8, 20, 20, 32, 32, 1, 1, 40] 201 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 48, 49, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 50]) total number of confs: 252 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114183 none COC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 118, 118, 64, 56, 16, 16, 16, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 118, 118, 118, 118, 118, 118, 118, 64, 64, 56, 56, 16, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8, 118] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 387 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114183 none COC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 7, 22, 22, 22, 40, 40, 40, 118, 118, 118, 160, 201, 201, 201, 201, 201, 118, 118, 40, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 22, 40, 40, 40, 40, 118, 160, 160, 201, 201, 40, 40, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 50, 33, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 723 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114183 none COC1=CC=C(CCC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 112, 102, 46, 46, 46, 32, 32, 32, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 32, 201, 201, 201, 201, 201, 201, 201, 112, 112, 102, 102, 46, 32, 32, 32, 32, 8, 4, 4, 2, 2, 32, 32, 201] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 617 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114183 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114183 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114183/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114183/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114183 Building REAL300020114184 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114184' /scratch/stefan/7770410/working/building/REAL300020114184 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114184 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114184/0 /scratch/stefan/7770410/working/building/REAL300020114184 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1985) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1985 `/scratch/stefan/7770410/working/3D/1985' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1CCOC2) `REAL300020114184.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114184 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1CCOC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 35, 98, 98, 63, 98, 98, 98, 98, 98, 98, 35, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 98, 98, 98, 98, 98, 98, 98, 98, 98] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 338 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114184 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1CCOC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 54, 54, 54, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 54, 107, 201, 201, 201, 201, 201, 201, 201, 201, 201, 107, 54, 54, 54, 54, 10, 6, 6, 4, 4, 54, 54, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 450 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114184 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1CCOC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 34, 49, 54, 54, 54, 54, 11, 11, 1, 6, 22, 22, 12, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 34, 34, 49, 49, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 276 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114184 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=CC2=C1CCOC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 22, 22, 22, 98, 98, 98, 165, 201, 201, 201, 201, 201, 98, 98, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 22, 22, 22, 22, 98, 165, 165, 201, 201, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 731 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114184 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114184/1 /scratch/stefan/7770410/working/building/REAL300020114184 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1986) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1986 `/scratch/stefan/7770410/working/3D/1986' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1CCOC2) `REAL300020114184.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114184/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114184 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1CCOC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 11, 11, 11, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 11, 35, 98, 98, 63, 98, 98, 98, 98, 98, 98, 35, 11, 11, 11, 11, 1, 6, 6, 8, 8, 11, 11, 98, 98, 98, 98, 98, 98, 98, 98, 98] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 338 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114184 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1CCOC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 54, 54, 54, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 54, 107, 201, 201, 201, 201, 201, 201, 201, 201, 201, 107, 54, 54, 54, 54, 10, 6, 6, 4, 4, 54, 54, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 450 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114184 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1CCOC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 34, 49, 54, 54, 54, 54, 11, 11, 1, 6, 22, 22, 12, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 11, 34, 34, 49, 49, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 276 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114184 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=CC2=C1CCOC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 22, 22, 22, 98, 98, 98, 165, 201, 201, 201, 201, 201, 98, 98, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 22, 22, 22, 22, 98, 165, 165, 201, 201, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 731 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114184 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114184 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114184/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114184/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114184 Building REAL300020114185 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114185' /scratch/stefan/7770410/working/building/REAL300020114185 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114185 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114185/0 /scratch/stefan/7770410/working/building/REAL300020114185 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1987) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1987 `/scratch/stefan/7770410/working/3D/1987' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2COCCC2=C1) `REAL300020114185.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114185 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2COCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 12, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 24, 72, 72, 72, 72, 72, 72, 72, 72, 72, 24, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 72, 72, 72, 72, 72, 72, 72, 72, 72] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 164 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114185 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2COCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 12, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 47, 47, 47, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 47, 78, 201, 201, 201, 201, 201, 201, 201, 201, 201, 78, 47, 47, 47, 47, 10, 6, 6, 4, 4, 47, 47, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 404 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114185 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2COCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 12, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 31, 45, 47, 47, 47, 47, 9, 9, 1, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 9, 31, 31, 45, 45, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114185 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2COCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 12, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 15, 15, 15, 72, 72, 72, 144, 201, 201, 201, 201, 201, 72, 72, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 72, 144, 144, 201, 201, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 822 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114185 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114185/1 /scratch/stefan/7770410/working/building/REAL300020114185 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1988) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1988 `/scratch/stefan/7770410/working/3D/1988' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2COCCC2=C1) `REAL300020114185.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114185/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114185 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2COCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 12, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 24, 72, 72, 72, 72, 72, 72, 72, 72, 72, 24, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 72, 72, 72, 72, 72, 72, 72, 72, 72] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 164 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114185 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2COCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 12, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 48, 48, 48, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 48, 79, 201, 201, 201, 201, 201, 201, 201, 201, 201, 79, 48, 48, 48, 48, 11, 6, 6, 4, 4, 48, 48, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 405 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114185 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2COCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 12, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 31, 45, 47, 47, 47, 47, 9, 9, 1, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 9, 31, 31, 45, 45, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114185 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2COCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 12, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 15, 15, 15, 72, 72, 72, 144, 201, 201, 201, 201, 201, 72, 72, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 72, 144, 144, 201, 201, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 822 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114185 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114185 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114185/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114185/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114185 Building REAL300020114186 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114186' /scratch/stefan/7770410/working/building/REAL300020114186 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114186 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114186/0 /scratch/stefan/7770410/working/building/REAL300020114186 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1989) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1989 `/scratch/stefan/7770410/working/3D/1989' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NO1) `REAL300020114186.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114186 none CC(C)(C)C1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 12, 23, 23, 12, 12, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 50, 70, 83, 83, 83, 83, 13, 13, 1, 12, 12, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 6, 1, 1, 1, 1, 13, 50, 50, 70, 70, 1, 1] 201 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 48, 49, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 374 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114186 none CC(C)(C)C1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 69, 100, 100, 69, 69, 54, 54, 54, 13, 13, 13, 1, 1, 1, 1, 1, 8, 10, 14, 14, 14, 14, 1, 1, 13, 69, 69, 100, 100, 100, 100, 100, 100, 100, 100, 100, 69, 54, 13, 13, 13, 13, 1, 8, 8, 10, 10, 13, 13] 201 rigid atoms, others: [43, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 375 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114186 none CC(C)(C)C1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 69, 69, 69, 147, 192, 201, 201, 201, 201, 69, 69, 12, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 12, 12, 12, 12, 69, 147, 147, 192, 192, 12, 12] 201 rigid atoms, others: [1, 4, 5, 6, 7, 26, 27, 37] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 767 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114186 none CC(C)(C)C1=CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 194, 194, 194, 85, 85, 85, 14, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 85, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 194, 85, 85, 85, 85, 14, 6, 6, 4, 4, 85, 85] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 550 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114186 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114186/1 /scratch/stefan/7770410/working/building/REAL300020114186 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1990) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1990 `/scratch/stefan/7770410/working/3D/1990' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NO1) `REAL300020114186.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114186/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114186 none CC(C)(C)C1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 12, 23, 23, 12, 12, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 52, 72, 86, 86, 86, 86, 13, 13, 1, 12, 12, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 6, 1, 1, 1, 1, 13, 52, 52, 72, 72, 1, 1] 201 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 48, 49, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 385 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114186 none CC(C)(C)C1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 69, 99, 99, 69, 69, 55, 55, 55, 13, 13, 13, 1, 1, 1, 1, 1, 9, 11, 15, 15, 15, 15, 1, 1, 13, 69, 69, 99, 99, 99, 99, 99, 99, 99, 99, 99, 69, 55, 13, 13, 13, 13, 1, 9, 9, 11, 11, 13, 13] 201 rigid atoms, others: [43, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 375 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114186 none CC(C)(C)C1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 69, 69, 69, 147, 192, 201, 201, 201, 201, 69, 69, 12, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 12, 12, 12, 12, 69, 147, 147, 192, 192, 12, 12] 201 rigid atoms, others: [1, 4, 5, 6, 7, 26, 27, 37] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 763 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114186 none CC(C)(C)C1=CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 194, 194, 194, 86, 86, 86, 15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 86, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 194, 86, 86, 86, 86, 15, 6, 6, 4, 4, 86, 86] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 549 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114186 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114186 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114186/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114186/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114186 Building REAL300020114187 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114187' /scratch/stefan/7770410/working/building/REAL300020114187 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114187 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114187/0 /scratch/stefan/7770410/working/building/REAL300020114187 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1991) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1991 `/scratch/stefan/7770410/working/3D/1991' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2CC1C1CC12) `REAL300020114187.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114187 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2CC1C1CC12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 17, 17, 17, 17, 1, 1, 13, 59, 86, 86, 86, 86, 86, 86, 86, 59, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 310 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114187 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2CC1C1CC12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 101, 101, 101, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 101, 173, 201, 201, 201, 201, 201, 201, 201, 173, 101, 101, 101, 101, 17, 6, 6, 4, 4, 101, 101, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 593 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114187 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2CC1C1CC12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 61, 85, 101, 101, 101, 101, 13, 13, 1, 6, 12, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 13, 61, 61, 85, 85, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 404 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114187 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CC2CC1C1CC12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 12, 12, 12, 86, 86, 86, 167, 201, 201, 201, 201, 201, 86, 86, 12, 1, 1, 1, 1, 1, 1, 1, 1, 4, 12, 12, 12, 12, 86, 167, 167, 201, 201, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 700 number of broken/clashed sets: 201 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114187 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114187/1 /scratch/stefan/7770410/working/building/REAL300020114187 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1992) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1992 `/scratch/stefan/7770410/working/3D/1992' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2CC1C1CC12) `REAL300020114187.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114187/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114187 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2CC1C1CC12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 13, 13, 13, 1, 1, 1, 1, 1, 9, 13, 18, 18, 18, 18, 1, 1, 13, 59, 85, 85, 85, 85, 85, 85, 85, 59, 13, 13, 13, 13, 1, 9, 9, 13, 13, 13, 13, 85, 85, 85, 85, 85, 85, 85, 85, 85, 85, 85] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 308 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114187 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2CC1C1CC12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 101, 101, 101, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 101, 173, 201, 201, 201, 201, 201, 201, 201, 173, 101, 101, 101, 101, 17, 6, 6, 4, 4, 101, 101, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 593 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114187 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2CC1C1CC12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 63, 87, 103, 103, 103, 103, 13, 13, 1, 6, 12, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 13, 63, 63, 87, 87, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 410 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114187 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CC2CC1C1CC12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 12, 12, 12, 85, 85, 85, 168, 201, 201, 201, 201, 201, 85, 85, 12, 1, 1, 1, 1, 1, 1, 1, 1, 4, 12, 12, 12, 12, 85, 168, 168, 201, 201, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 699 number of broken/clashed sets: 201 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114187 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114187 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114187/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114187/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114187 Building REAL300020114188 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114188' /scratch/stefan/7770410/working/building/REAL300020114188 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114188 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114188/0 /scratch/stefan/7770410/working/building/REAL300020114188 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1993) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1993 `/scratch/stefan/7770410/working/3D/1993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)O1) `REAL300020114188.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114188 none CC1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 35, 52, 57, 57, 57, 57, 13, 13, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 13, 35, 35, 52, 52, 1, 1, 26, 26, 26, 26] 201 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 43, 44, 22] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48]) total number of confs: 284 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114188 none CC1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [126, 126, 126, 56, 56, 56, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 13, 126, 126, 126, 126, 126, 126, 126, 126, 126, 126, 56, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 126, 126, 126, 126] 201 rigid atoms, others: [38, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 378 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114188 none CC1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 8, 26, 26, 26, 126, 126, 126, 176, 201, 201, 201, 201, 201, 126, 126, 26, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 8, 26, 26, 26, 26, 126, 176, 176, 201, 201, 26, 26, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 32, 45, 23, 24, 25, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48]) total number of confs: 612 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114188 none CC1CC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 144, 144, 144, 57, 57, 57, 9, 9, 9, 6, 4, 1, 1, 1, 1, 1, 1, 9, 9, 57, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 144, 57, 57, 57, 57, 9, 6, 6, 4, 4, 57, 57, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 590 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114188 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114188/1 /scratch/stefan/7770410/working/building/REAL300020114188 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1994) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1994 `/scratch/stefan/7770410/working/3D/1994' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)O1) `REAL300020114188.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114188/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114188 none CC1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 35, 52, 57, 57, 57, 57, 13, 13, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 13, 35, 35, 52, 52, 1, 1, 26, 26, 26, 26] 201 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 43, 44, 22] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48]) total number of confs: 284 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114188 none CC1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [126, 126, 126, 56, 56, 56, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 13, 126, 126, 126, 126, 126, 126, 126, 126, 126, 126, 56, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 126, 126, 126, 126] 201 rigid atoms, others: [38, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 378 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114188 none CC1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 8, 26, 26, 26, 126, 126, 126, 176, 201, 201, 201, 201, 201, 126, 126, 26, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 8, 26, 26, 26, 26, 126, 176, 176, 201, 201, 26, 26, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 32, 45, 23, 24, 25, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48]) total number of confs: 612 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114188 none CC1CC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 144, 144, 144, 57, 57, 57, 9, 9, 9, 6, 4, 1, 1, 1, 1, 1, 1, 9, 9, 57, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 144, 57, 57, 57, 57, 9, 6, 6, 4, 4, 57, 57, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 590 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114188 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114188 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114188/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114188/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114188 Building REAL300020114189 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114189' /scratch/stefan/7770410/working/building/REAL300020114189 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114189 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114189/0 /scratch/stefan/7770410/working/building/REAL300020114189 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1995) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1995 `/scratch/stefan/7770410/working/3D/1995' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C(F)F)N=CS1) `REAL300020114189.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114189 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C(F)F)N=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 38, 85, 85, 109, 109, 85, 85, 85, 38, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 109, 85] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 338 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114189 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C(F)F)N=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [123, 123, 49, 49, 49, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 49, 123, 201, 201, 201, 201, 201, 201, 201, 123, 49, 49, 49, 49, 10, 6, 6, 4, 4, 49, 49, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 479 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114189 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C(F)F)N=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 48, 53, 53, 53, 53, 11, 11, 1, 6, 15, 15, 31, 31, 15, 15, 15, 6, 1, 1, 1, 1, 11, 33, 33, 48, 48, 1, 1, 31, 15] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114189 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=C(C(F)F)N=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 15, 15, 15, 85, 85, 85, 155, 201, 201, 201, 201, 201, 85, 85, 15, 1, 1, 1, 5, 5, 1, 1, 1, 4, 15, 15, 15, 15, 85, 155, 155, 201, 201, 15, 15, 5, 1] 201 rigid atoms, others: [1, 40, 19, 20, 21, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 769 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114189 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114189/1 /scratch/stefan/7770410/working/building/REAL300020114189 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1996) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1996 `/scratch/stefan/7770410/working/3D/1996' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C(F)F)N=CS1) `REAL300020114189.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114189 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C(F)F)N=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 11, 11, 11, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 1, 1, 11, 38, 83, 83, 107, 107, 83, 83, 83, 38, 11, 11, 11, 11, 1, 7, 7, 9, 9, 11, 11, 107, 83] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 333 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114189 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C(F)F)N=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 124, 49, 49, 49, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 49, 124, 201, 201, 201, 201, 201, 201, 201, 124, 49, 49, 49, 49, 10, 6, 6, 4, 4, 49, 49, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 479 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114189 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C(F)F)N=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 33, 48, 54, 54, 54, 54, 11, 11, 1, 6, 15, 15, 30, 30, 15, 15, 15, 6, 1, 1, 1, 1, 11, 33, 33, 48, 48, 1, 1, 30, 15] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 18, 37, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 296 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114189 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=C(C(F)F)N=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 15, 15, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 15, 15, 15, 83, 83, 83, 153, 200, 201, 201, 201, 201, 83, 83, 15, 1, 1, 1, 5, 5, 1, 1, 1, 4, 15, 15, 15, 15, 83, 153, 153, 200, 200, 15, 15, 5, 1] 201 rigid atoms, others: [1, 40, 19, 20, 21, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 775 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114189 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114189 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114189/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114189/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114189 Building REAL300020114190 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114190' /scratch/stefan/7770410/working/building/REAL300020114190 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114190 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114190/0 /scratch/stefan/7770410/working/building/REAL300020114190 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1997) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1997 `/scratch/stefan/7770410/working/3D/1997' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCCC1) `REAL300020114190.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114190 none COC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 58, 24, 24, 24, 6, 6, 6, 1, 1, 1, 1, 1, 8, 10, 15, 15, 15, 15, 1, 1, 6, 58, 98, 99, 99, 99, 99, 66, 66, 66, 58, 24, 6, 6, 6, 6, 1, 8, 8, 10, 10, 6, 6, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99] 201 rigid atoms, others: [37, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 409 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114190 none COC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [166, 164, 112, 112, 112, 49, 49, 49, 16, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 49, 164, 201, 201, 201, 201, 201, 166, 166, 166, 164, 112, 49, 49, 49, 49, 16, 6, 6, 4, 4, 49, 49, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 713 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114190 none COC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 21, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 29, 33, 47, 47, 47, 47, 6, 6, 1, 21, 46, 47, 47, 47, 47, 29, 29, 29, 21, 6, 1, 1, 1, 1, 6, 29, 29, 33, 33, 1, 1, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 42, 43, 21] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114190 none COC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 8, 1, 8, 23, 23, 23, 47, 47, 47, 99, 99, 99, 190, 201, 201, 201, 201, 201, 99, 99, 47, 1, 1, 1, 1, 1, 1, 11, 11, 11, 8, 23, 47, 47, 47, 47, 99, 190, 190, 201, 201, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 54, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 22, 23, 24, 25, 26, 27] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 733 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114190 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114190/1 /scratch/stefan/7770410/working/building/REAL300020114190 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 1998) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1998 `/scratch/stefan/7770410/working/3D/1998' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCCC1) `REAL300020114190.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114190 none COC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 58, 24, 24, 24, 6, 6, 6, 1, 1, 1, 1, 1, 8, 10, 15, 15, 15, 15, 1, 1, 6, 58, 99, 100, 100, 100, 100, 66, 66, 66, 58, 24, 6, 6, 6, 6, 1, 8, 8, 10, 10, 6, 6, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100] 201 rigid atoms, others: [37, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 411 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114190 none COC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [166, 164, 114, 114, 114, 50, 50, 50, 16, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 50, 164, 201, 201, 201, 201, 201, 166, 166, 166, 164, 114, 50, 50, 50, 50, 16, 6, 6, 4, 4, 50, 50, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 708 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114190 none COC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 21, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 30, 34, 49, 49, 49, 49, 6, 6, 1, 21, 46, 47, 47, 47, 47, 29, 29, 29, 21, 6, 1, 1, 1, 1, 6, 30, 30, 34, 34, 1, 1, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 42, 43, 21] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114190 none COC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 8, 1, 8, 23, 23, 23, 47, 47, 47, 100, 100, 100, 190, 201, 201, 201, 201, 201, 100, 100, 47, 1, 1, 1, 1, 1, 1, 11, 11, 11, 8, 23, 47, 47, 47, 47, 100, 190, 190, 201, 201, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 54, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 22, 23, 24, 25, 26, 27] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 723 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114190 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114190 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114190/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114190/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114190 Building REAL300020114191 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114191' /scratch/stefan/7770410/working/building/REAL300020114191 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114191 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114191/0 /scratch/stefan/7770410/working/building/REAL300020114191 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 1999) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/1999 `/scratch/stefan/7770410/working/3D/1999' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1CC) `REAL300020114191.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114191 none CCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 5, 3, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 7, 7, 7, 19, 28, 28, 28, 28, 28, 7, 7, 1, 9, 9, 9, 17, 17, 17, 17, 17, 17, 9, 9, 3, 1, 1, 1, 1, 7, 19, 19, 28, 28, 1, 1, 9, 17, 17, 17, 17, 17] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 46, 47, 40, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50, 51, 52, 53]) total number of confs: 240 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114191 none CCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 25, 13, 48, 48, 13, 13, 13, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 48, 48, 48, 95, 95, 95, 95, 95, 95, 48, 48, 13, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7, 48, 95, 95, 95, 95, 95] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 763 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114191 none CCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 48, 48, 48, 80, 103, 103, 103, 103, 103, 48, 48, 9, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 5, 9, 9, 9, 9, 48, 80, 80, 103, 103, 9, 9, 1, 3, 3, 3, 3, 3] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 2, 48, 35, 25, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53]) total number of confs: 395 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114191 none CCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)C=C1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 59, 33, 103, 103, 33, 33, 33, 28, 28, 28, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 28, 103, 103, 103, 201, 201, 201, 201, 201, 201, 103, 103, 33, 28, 28, 28, 28, 8, 4, 4, 2, 2, 28, 28, 103, 201, 201, 201, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 1553 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114191 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114191/1 /scratch/stefan/7770410/working/building/REAL300020114191 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 2000) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/2000 `/scratch/stefan/7770410/working/3D/2000' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1CC) `REAL300020114191.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114191 none CCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 5, 3, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 7, 7, 7, 19, 28, 28, 28, 28, 28, 7, 7, 1, 9, 9, 9, 17, 17, 17, 17, 17, 17, 9, 9, 3, 1, 1, 1, 1, 7, 19, 19, 28, 28, 1, 1, 9, 17, 17, 17, 17, 17] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 46, 47, 40, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 48, 49, 50, 51, 52, 53]) total number of confs: 240 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114191 none CCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 25, 13, 49, 49, 13, 13, 13, 7, 7, 7, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 7, 49, 49, 49, 97, 97, 97, 97, 97, 97, 49, 49, 13, 7, 7, 7, 7, 1, 6, 6, 8, 8, 7, 7, 49, 97, 97, 97, 97, 97] 201 rigid atoms, others: [41, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 777 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114191 none CCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 49, 49, 49, 80, 103, 103, 103, 103, 103, 49, 49, 9, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 5, 9, 9, 9, 9, 49, 80, 80, 103, 103, 9, 9, 1, 3, 3, 3, 3, 3] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 2, 48, 35, 25, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53]) total number of confs: 393 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114191 none CCC1=CC=C(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)C=C1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 59, 33, 103, 103, 33, 33, 33, 28, 28, 28, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 28, 103, 103, 103, 201, 201, 201, 201, 201, 201, 103, 103, 33, 28, 28, 28, 28, 8, 4, 4, 2, 2, 28, 28, 103, 201, 201, 201, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 1553 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114191 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114191 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114191/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114191/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114191 Building REAL300020114192 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114192' /scratch/stefan/7770410/working/building/REAL300020114192 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114192 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114192/0 /scratch/stefan/7770410/working/building/REAL300020114192 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 2001) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/2001 `/scratch/stefan/7770410/working/3D/2001' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC=CC=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114192.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114192 none COCC1=CC=CC=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 40, 23, 23, 23, 23, 23, 23, 23, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 35, 35, 35, 35, 8, 8, 1, 53, 53, 53, 40, 40, 23, 23, 23, 23, 23, 23, 5, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 336 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114192 none COCC1=CC=CC=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [134, 125, 86, 86, 86, 86, 86, 86, 86, 20, 20, 20, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 134, 134, 134, 125, 125, 86, 86, 86, 86, 86, 86, 20, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 563 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114192 none COCC1=CC=CC=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 9, 9, 9, 23, 23, 23, 86, 86, 86, 149, 188, 188, 188, 188, 188, 86, 86, 23, 10, 10, 10, 5, 5, 1, 1, 1, 1, 3, 3, 9, 23, 23, 23, 23, 86, 149, 149, 188, 188, 23, 23] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 2, 35, 36, 37] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 725 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114192 none COCC1=CC=CC=C1CC(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 197, 197, 197, 197, 197, 197, 197, 60, 60, 60, 37, 37, 37, 10, 10, 10, 4, 2, 1, 1, 1, 1, 1, 1, 10, 10, 37, 201, 201, 201, 201, 201, 197, 197, 197, 197, 197, 197, 60, 37, 37, 37, 37, 10, 4, 4, 2, 2, 37, 37] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 744 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114192 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114192/1 /scratch/stefan/7770410/working/building/REAL300020114192 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 2002) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/2002 `/scratch/stefan/7770410/working/3D/2002' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC=CC=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114192.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114192 none COCC1=CC=CC=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 40, 23, 23, 23, 23, 23, 23, 23, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 23, 35, 35, 35, 35, 35, 8, 8, 1, 53, 53, 53, 40, 40, 23, 23, 23, 23, 23, 23, 5, 1, 1, 1, 1, 8, 23, 23, 35, 35, 1, 1] 201 rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 50, 51, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 336 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114192 none COCC1=CC=CC=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [134, 124, 85, 85, 85, 85, 85, 85, 85, 20, 20, 20, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 8, 134, 134, 134, 124, 124, 85, 85, 85, 85, 85, 85, 20, 8, 8, 8, 8, 1, 6, 6, 8, 8, 8, 8] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 562 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114192 none COCC1=CC=CC=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 9, 9, 9, 23, 23, 23, 85, 85, 85, 148, 188, 188, 188, 188, 188, 85, 85, 23, 10, 10, 10, 5, 5, 1, 1, 1, 1, 3, 3, 9, 23, 23, 23, 23, 85, 148, 148, 188, 188, 23, 23] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 2, 35, 36, 37] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 730 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114192 none COCC1=CC=CC=C1CC(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 197, 197, 197, 197, 197, 197, 197, 60, 60, 60, 36, 36, 36, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 36, 201, 201, 201, 201, 201, 197, 197, 197, 197, 197, 197, 60, 36, 36, 36, 36, 9, 4, 4, 2, 2, 36, 36] 201 rigid atoms, others: [20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 747 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114192 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114192 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114192/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114192/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114192 Building REAL300020114193 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114193' /scratch/stefan/7770410/working/building/REAL300020114193 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114193 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114193/0 /scratch/stefan/7770410/working/building/REAL300020114193 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 2003) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/2003 `/scratch/stefan/7770410/working/3D/2003' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCS1(=O)=O) `REAL300020114193.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114193 none CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCS1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 14, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 50, 69, 87, 87, 87, 87, 12, 12, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 12, 50, 50, 69, 69, 1, 1, 17, 17, 17, 17, 17, 17] 201 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 41, 40, 20, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47]) total number of confs: 351 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114193 none CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCS1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 14, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 47, 47, 47, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 12, 88, 88, 88, 88, 88, 88, 88, 88, 88, 47, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 88, 88, 88, 88, 88, 88] 201 rigid atoms, others: [35, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 302 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114193 none CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCS1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 14, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 6, 6, 6, 17, 17, 17, 88, 88, 88, 163, 201, 201, 201, 201, 201, 88, 88, 17, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 17, 17, 17, 17, 88, 163, 163, 201, 201, 17, 17, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 42, 43, 44, 45, 46, 47, 21, 22, 23, 24, 25, 26] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 735 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114193 none CC1(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCS1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 14, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 162, 162, 162, 87, 87, 87, 16, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 87, 201, 201, 201, 201, 201, 201, 201, 201, 201, 162, 87, 87, 87, 87, 16, 6, 6, 4, 4, 87, 87, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 607 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114193 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114193/1 /scratch/stefan/7770410/working/building/REAL300020114193 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 2004) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/2004 `/scratch/stefan/7770410/working/3D/2004' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCS1(=O)=O) `REAL300020114193.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114193/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114193 none CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCS1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 14, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 50, 69, 87, 87, 87, 87, 12, 12, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 12, 50, 50, 69, 69, 1, 1, 18, 18, 18, 18, 18, 18] 201 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 41, 40, 20, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47]) total number of confs: 353 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114193 none CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCS1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 14, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 47, 47, 47, 12, 12, 12, 1, 1, 1, 1, 1, 9, 11, 16, 16, 16, 16, 1, 1, 12, 89, 89, 89, 89, 89, 89, 89, 89, 89, 47, 12, 12, 12, 12, 1, 9, 9, 11, 11, 12, 12, 89, 89, 89, 89, 89, 89] 201 rigid atoms, others: [35, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 304 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114193 none CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCS1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 14, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 6, 6, 6, 18, 18, 18, 89, 89, 89, 163, 201, 201, 201, 201, 201, 89, 89, 18, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 18, 18, 18, 18, 89, 163, 163, 201, 201, 18, 18, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 42, 43, 44, 45, 46, 47, 21, 22, 23, 24, 25, 26] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 733 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114193 none CC1(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCS1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 14, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 161, 161, 161, 88, 88, 88, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 88, 201, 201, 201, 201, 201, 201, 201, 201, 201, 161, 88, 88, 88, 88, 17, 6, 6, 4, 4, 88, 88, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 605 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114193 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114193 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114193/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114193/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114193 Building REAL300020114194 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114194' /scratch/stefan/7770410/working/building/REAL300020114194 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114194 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114194/0 /scratch/stefan/7770410/working/building/REAL300020114194 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 2005) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/2005 `/scratch/stefan/7770410/working/3D/2005' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C(C)O1) `REAL300020114194.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114194 none CCC1=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 40, 58, 60, 60, 60, 60, 12, 12, 1, 6, 6, 6, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 12, 40, 40, 58, 58, 1, 1, 6, 6, 6] 201 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 320 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114194 none CCC1=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 48, 48, 48, 48, 48, 48, 12, 12, 12, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 12, 48, 48, 48, 110, 110, 110, 110, 110, 48, 12, 12, 12, 12, 1, 6, 6, 8, 8, 12, 12, 48, 48, 48] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 457 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114194 none CCC1=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 48, 48, 48, 129, 184, 186, 186, 186, 186, 48, 48, 6, 1, 1, 1, 8, 8, 8, 7, 7, 2, 6, 6, 6, 6, 48, 129, 129, 184, 184, 6, 6, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 44, 45, 46, 24, 25, 26] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 777 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114194 none CCC1=NC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 186, 186, 186, 186, 186, 186, 60, 60, 60, 10, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 60, 186, 186, 186, 201, 201, 201, 201, 201, 186, 60, 60, 60, 60, 10, 6, 6, 4, 4, 60, 60, 186, 186, 186] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 579 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114194 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114194/1 /scratch/stefan/7770410/working/building/REAL300020114194 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 2006) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/2006 `/scratch/stefan/7770410/working/3D/2006' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C(C)O1) `REAL300020114194.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114194 none CCC1=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 40, 57, 59, 59, 59, 59, 12, 12, 1, 6, 6, 6, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 12, 40, 40, 57, 57, 1, 1, 6, 6, 6] 201 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 314 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114194 none CCC1=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 48, 48, 48, 48, 48, 48, 12, 12, 12, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 12, 48, 48, 48, 110, 110, 110, 110, 110, 48, 12, 12, 12, 12, 1, 6, 6, 8, 8, 12, 12, 48, 48, 48] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 460 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114194 none CCC1=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 48, 48, 48, 130, 184, 186, 186, 186, 186, 48, 48, 6, 1, 1, 1, 8, 8, 8, 7, 7, 2, 6, 6, 6, 6, 48, 130, 130, 184, 184, 6, 6, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 44, 45, 46, 24, 25, 26] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 774 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114194 none CCC1=NC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 187, 187, 187, 187, 187, 187, 60, 60, 60, 11, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 60, 187, 187, 187, 201, 201, 201, 201, 201, 187, 60, 60, 60, 60, 11, 6, 6, 4, 4, 60, 60, 187, 187, 187] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 577 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114194 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114194 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114194/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114194/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114194 Building REAL300020114195 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114195' /scratch/stefan/7770410/working/building/REAL300020114195 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114195 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114195/0 /scratch/stefan/7770410/working/building/REAL300020114195 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 2007) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/2007 `/scratch/stefan/7770410/working/3D/2007' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(C)(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114195.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114195 none CC(=O)NCC(C)(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 104, 109, 71, 47, 20, 47, 47, 20, 20, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 109, 109, 109, 109, 71, 71, 47, 47, 47, 47, 47, 47, 20, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [44, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 492 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114195 none CC(=O)NCC(C)(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 195, 201, 177, 129, 61, 129, 129, 61, 61, 35, 35, 35, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 35, 201, 201, 201, 201, 177, 177, 129, 129, 129, 129, 129, 129, 61, 35, 35, 35, 35, 9, 4, 4, 2, 2, 35, 35] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 900 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114195 none CC(=O)NCC(C)(C)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 36, 37, 22, 11, 5, 11, 11, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 21, 33, 33, 33, 33, 33, 7, 7, 1, 37, 37, 37, 37, 22, 22, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 7, 21, 21, 33, 33, 1, 1] 201 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 49, 50, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114195 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114195/1 /scratch/stefan/7770410/working/building/REAL300020114195 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 2008) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/2008 `/scratch/stefan/7770410/working/3D/2008' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(C)(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114195.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114195 none CC(=O)NCC(C)(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 103, 108, 70, 46, 19, 46, 46, 19, 19, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 108, 108, 108, 108, 70, 70, 46, 46, 46, 46, 46, 46, 19, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [44, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 490 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114195 none CC(=O)NCC(C)(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 195, 201, 178, 130, 61, 130, 130, 61, 61, 35, 35, 35, 9, 9, 9, 4, 2, 1, 1, 1, 1, 1, 1, 9, 9, 35, 201, 201, 201, 201, 178, 178, 130, 130, 130, 130, 130, 130, 61, 35, 35, 35, 35, 9, 4, 4, 2, 2, 35, 35] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 901 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114195 none CC(=O)NCC(C)(C)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 36, 37, 22, 11, 5, 11, 11, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 21, 33, 33, 33, 33, 33, 7, 7, 1, 37, 37, 37, 37, 22, 22, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 7, 21, 21, 33, 33, 1, 1] 201 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 49, 50, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114195 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114195 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114195/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114195/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114195 Building REAL300020114196 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114196' /scratch/stefan/7770410/working/building/REAL300020114196 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114196 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114196/0 /scratch/stefan/7770410/working/building/REAL300020114196 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 2009) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/2009 `/scratch/stefan/7770410/working/3D/2009' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(C)C(C)(C)C) `REAL300020114196.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114196 none CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(C)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 51, 51, 51, 12, 12, 12, 1, 1, 1, 1, 1, 8, 10, 15, 15, 15, 15, 1, 1, 12, 76, 76, 76, 82, 82, 82, 76, 76, 76, 76, 51, 12, 12, 12, 12, 1, 8, 8, 10, 10, 12, 12, 76, 76, 76, 76, 82, 82, 82, 82, 82, 82, 82, 82, 82] 201 rigid atoms, others: [36, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 355 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114196 none CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(C)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 163, 163, 163, 83, 83, 83, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 83, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 163, 83, 83, 83, 83, 17, 6, 6, 4, 4, 83, 83, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 671 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114196 none CC(C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C(C)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 52, 70, 82, 82, 82, 82, 12, 12, 1, 11, 11, 11, 15, 15, 15, 11, 11, 11, 11, 6, 1, 1, 1, 1, 12, 52, 52, 70, 70, 1, 1, 11, 11, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 41, 42, 20] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 361 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114196 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114196/1 /scratch/stefan/7770410/working/building/REAL300020114196 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 2010) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/2010 `/scratch/stefan/7770410/working/3D/2010' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(C)C(C)(C)C) `REAL300020114196.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114196/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114196 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(C)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 51, 51, 51, 12, 12, 12, 1, 1, 1, 1, 1, 8, 10, 15, 15, 15, 15, 1, 1, 12, 76, 76, 76, 83, 83, 83, 76, 76, 76, 76, 51, 12, 12, 12, 12, 1, 8, 8, 10, 10, 12, 12, 76, 76, 76, 76, 83, 83, 83, 83, 83, 83, 83, 83, 83] 201 rigid atoms, others: [36, 7, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 361 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114196 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(C)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 163, 163, 163, 83, 83, 83, 17, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 83, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 163, 83, 83, 83, 83, 17, 6, 6, 4, 4, 83, 83, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 667 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114196 none CC(C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C(C)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 52, 70, 82, 82, 82, 82, 12, 12, 1, 11, 11, 11, 15, 15, 15, 11, 11, 11, 11, 6, 1, 1, 1, 1, 12, 52, 52, 70, 70, 1, 1, 11, 11, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 41, 42, 20] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 361 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114196 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114196 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114196/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114196/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114196 Building REAL300020114197 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114197' /scratch/stefan/7770410/working/building/REAL300020114197 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114197 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114197/0 /scratch/stefan/7770410/working/building/REAL300020114197 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 2011) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/2011 `/scratch/stefan/7770410/working/3D/2011' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CC=CO1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114197.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114197 none CC(CC1=CC=CO1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 5, 17, 24, 34, 34, 34, 34, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 26, 39, 41, 41, 41, 41, 9, 9, 1, 17, 17, 17, 17, 24, 24, 34, 34, 34, 5, 1, 1, 1, 1, 9, 26, 26, 39, 39, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 276 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114197 none CC(CC1=CC=CO1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 25, 73, 94, 117, 117, 117, 117, 25, 25, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 9, 73, 73, 73, 73, 94, 94, 117, 117, 117, 25, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 464 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114197 none CC(CC1=CC=CO1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 34, 34, 34, 117, 117, 117, 173, 201, 201, 201, 201, 201, 117, 117, 34, 7, 7, 7, 7, 3, 3, 1, 1, 1, 17, 34, 34, 34, 34, 117, 173, 173, 201, 201, 34, 34] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 35] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 690 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114197 none CC(CC1=CC=CO1)C(=O)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [175, 77, 175, 186, 201, 201, 201, 201, 77, 77, 40, 40, 40, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 40, 175, 175, 175, 175, 186, 186, 201, 201, 201, 77, 40, 40, 40, 40, 9, 5, 5, 3, 3, 40, 40] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 764 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114197 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114197/1 /scratch/stefan/7770410/working/building/REAL300020114197 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 2012) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/2012 `/scratch/stefan/7770410/working/3D/2012' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CC=CO1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114197.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114197/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114197 none CC(CC1=CC=CO1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 5, 17, 24, 33, 33, 33, 33, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 26, 39, 41, 41, 41, 41, 10, 10, 1, 17, 17, 17, 17, 24, 24, 33, 33, 33, 5, 1, 1, 1, 1, 10, 26, 26, 39, 39, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 47, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 272 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114197 none CC(CC1=CC=CO1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 26, 73, 94, 117, 117, 117, 117, 26, 26, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 10, 73, 73, 73, 73, 94, 94, 117, 117, 117, 26, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 462 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114197 none CC(CC1=CC=CO1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 33, 33, 33, 117, 117, 117, 173, 201, 201, 201, 201, 201, 117, 117, 33, 7, 7, 7, 7, 3, 3, 1, 1, 1, 16, 33, 33, 33, 33, 117, 173, 173, 201, 201, 33, 33] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 35] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 693 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114197 none CC(CC1=CC=CO1)C(=O)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [175, 76, 175, 186, 201, 201, 201, 201, 76, 76, 40, 40, 40, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 40, 175, 175, 175, 175, 186, 186, 201, 201, 201, 76, 40, 40, 40, 40, 9, 5, 5, 3, 3, 40, 40] 201 rigid atoms, others: [18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 768 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114197 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114197 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114197/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114197/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114197 Building REAL300020114198 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114198' /scratch/stefan/7770410/working/building/REAL300020114198 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114198 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114198/0 /scratch/stefan/7770410/working/building/REAL300020114198 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 2013) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/2013 `/scratch/stefan/7770410/working/3D/2013' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC1=NNC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1) `REAL300020114198.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114198 none CCCCCC1=NNC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 21, 8, 8, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 26, 40, 40, 40, 40, 40, 10, 10, 1, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 21, 21, 8, 6, 1, 1, 1, 1, 10, 26, 26, 40, 40, 1, 1, 8] 201 rigid atoms, others: [45, 43, 44, 42, 11, 12, 13, 14, 15, 51, 52, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50, 53]) total number of confs: 269 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114198 none CCCCCC1=NNC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 86, 33, 33, 33, 33, 30, 30, 30, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 10, 33, 99, 99, 99, 99, 99, 99, 99, 99, 99, 86, 86, 33, 30, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 33] 201 rigid atoms, others: [46, 15, 16, 17, 18, 14, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 401 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114198 none CCCCCC1=NNC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 7, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 33, 33, 33, 62, 82, 82, 82, 82, 82, 33, 33, 8, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 1, 4, 8, 8, 8, 8, 33, 62, 62, 82, 82, 8, 8, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 40, 53, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 350 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114198 none CCCCCC1=NNC(C(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 188, 85, 85, 85, 85, 81, 81, 81, 40, 40, 40, 9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 40, 85, 201, 201, 201, 201, 201, 201, 201, 201, 201, 188, 188, 85, 81, 40, 40, 40, 40, 9, 5, 5, 3, 3, 40, 40, 85] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 758 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114198 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114198/1 /scratch/stefan/7770410/working/building/REAL300020114198 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 2014) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/2014 `/scratch/stefan/7770410/working/3D/2014' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC1=NNC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1) `REAL300020114198.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114198 none CCCCCC1=NNC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 21, 8, 8, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 10, 26, 40, 41, 41, 41, 41, 10, 10, 1, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 21, 21, 8, 6, 1, 1, 1, 1, 10, 26, 26, 40, 40, 1, 1, 8] 201 rigid atoms, others: [45, 43, 44, 42, 11, 12, 13, 14, 15, 51, 52, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50, 53]) total number of confs: 271 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114198 none CCCCCC1=NNC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 86, 33, 33, 33, 33, 30, 30, 30, 10, 10, 10, 1, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 1, 1, 10, 33, 99, 99, 99, 99, 99, 99, 99, 99, 99, 86, 86, 33, 30, 10, 10, 10, 10, 1, 6, 6, 8, 8, 10, 10, 33] 201 rigid atoms, others: [46, 15, 16, 17, 18, 14, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 403 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114198 none CCCCCC1=NNC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 7, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 33, 33, 33, 62, 82, 83, 83, 83, 83, 33, 33, 8, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 1, 4, 8, 8, 8, 8, 33, 62, 62, 82, 82, 8, 8, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 40, 53, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 352 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114198 none CCCCCC1=NNC(C(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 188, 83, 83, 83, 83, 80, 80, 80, 41, 41, 41, 10, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 41, 83, 201, 201, 201, 201, 201, 201, 201, 201, 201, 188, 188, 83, 80, 41, 41, 41, 41, 10, 5, 5, 3, 3, 41, 41, 83] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 759 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114198 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114198 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114198/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114198/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114198 Building REAL300020114199 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114199' /scratch/stefan/7770410/working/building/REAL300020114199 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114199 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114199/0 /scratch/stefan/7770410/working/building/REAL300020114199 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 2015) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/2015 `/scratch/stefan/7770410/working/3D/2015' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC1(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCCC1) `REAL300020114199.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114199 none C=CC1(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 39, 17, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 23, 31, 31, 31, 31, 31, 13, 13, 1, 39, 39, 39, 39, 39, 45, 45, 45, 17, 17, 6, 1, 1, 1, 1, 13, 23, 23, 31, 31, 1, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 201 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 43, 44, 22] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 264 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114199 none C=CC1(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 97, 51, 51, 51, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 13, 157, 157, 157, 157, 157, 157, 157, 157, 97, 97, 51, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 157, 157, 157, 157, 157, 157, 157, 157, 157, 157] 201 rigid atoms, others: [38, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 623 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114199 none C=CC1(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 9, 15, 15, 15, 39, 39, 39, 157, 157, 157, 181, 201, 201, 201, 201, 201, 157, 157, 39, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 15, 39, 39, 39, 39, 157, 181, 181, 201, 201, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 23, 24, 25, 26, 27] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 511 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114199 none C=CC1(CC(=O)NC2CC(N3C=C(CCC4=N[N-]N=N4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 154, 96, 96, 96, 36, 36, 36, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 36, 201, 201, 201, 201, 201, 201, 201, 201, 154, 154, 96, 36, 36, 36, 36, 7, 4, 4, 2, 2, 36, 36, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 794 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114199 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114199/1 /scratch/stefan/7770410/working/building/REAL300020114199 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 2016) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/2016 `/scratch/stefan/7770410/working/3D/2016' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC1(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCCC1) `REAL300020114199.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114199/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114199 none C=CC1(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 39, 17, 6, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13, 23, 31, 31, 31, 31, 31, 13, 13, 1, 39, 39, 39, 39, 39, 45, 45, 45, 17, 17, 6, 1, 1, 1, 1, 13, 23, 23, 31, 31, 1, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 201 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 43, 44, 22] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 264 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114199 none C=CC1(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 97, 51, 51, 51, 13, 13, 13, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 13, 157, 157, 157, 157, 157, 157, 157, 157, 97, 97, 51, 13, 13, 13, 13, 1, 5, 5, 7, 7, 13, 13, 157, 157, 157, 157, 157, 157, 157, 157, 157, 157] 201 rigid atoms, others: [38, 9, 10, 11, 12, 13, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 623 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114199 none C=CC1(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 9, 15, 15, 15, 39, 39, 39, 157, 157, 157, 181, 201, 201, 201, 201, 201, 157, 157, 39, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 15, 39, 39, 39, 39, 157, 181, 181, 201, 201, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 23, 24, 25, 26, 27] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 511 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114199 none C=CC1(CC(=O)NC2CC(N3C=C(CCC4=NN=N[N-]4)N=N3)C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 155, 97, 97, 97, 37, 37, 37, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 37, 201, 201, 201, 201, 201, 201, 201, 201, 155, 155, 97, 37, 37, 37, 37, 7, 4, 4, 2, 2, 37, 37, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 792 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114199 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114199 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114199/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114199/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114199 Building REAL300020114200 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114200' /scratch/stefan/7770410/working/building/REAL300020114200 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114200 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114200/0 /scratch/stefan/7770410/working/building/REAL300020114200 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 2017) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/2017 `/scratch/stefan/7770410/working/3D/2017' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2CCC=CC2=C1) `REAL300020114200.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114200 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2CCC=CC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 24, 74, 74, 74, 74, 74, 74, 74, 74, 74, 24, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 74, 74, 74, 74, 74, 74, 74, 74, 74] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 166 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114200 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2CCC=CC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 47, 47, 47, 12, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 47, 76, 201, 201, 201, 201, 201, 201, 201, 201, 201, 76, 47, 47, 47, 47, 12, 6, 6, 4, 4, 47, 47, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 395 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114200 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2CCC=CC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 29, 42, 45, 45, 45, 45, 9, 9, 1, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 9, 29, 29, 42, 42, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114200 none O=C(NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1)C1=CC=C2CCC=CC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 16, 16, 16, 74, 74, 74, 146, 201, 201, 201, 201, 201, 74, 74, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 74, 146, 146, 201, 201, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 810 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114200 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114200/1 /scratch/stefan/7770410/working/building/REAL300020114200 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 2018) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/2018 `/scratch/stefan/7770410/working/3D/2018' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2CCC=CC2=C1) `REAL300020114200.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114200/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114200 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2CCC=CC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 9, 9, 9, 1, 1, 1, 1, 1, 6, 8, 10, 10, 10, 10, 1, 1, 9, 25, 74, 74, 74, 74, 74, 74, 74, 74, 74, 25, 9, 9, 9, 9, 1, 6, 6, 8, 8, 9, 9, 74, 74, 74, 74, 74, 74, 74, 74, 74] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 16, 17] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 167 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114200 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2CCC=CC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 48, 48, 48, 13, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 48, 77, 201, 201, 201, 201, 201, 201, 201, 201, 201, 77, 48, 48, 48, 48, 13, 6, 6, 4, 4, 48, 48, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 394 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114200 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2CCC=CC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 30, 43, 46, 46, 46, 46, 9, 9, 1, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 9, 30, 30, 43, 43, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 39, 40, 18, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114200 none O=C(NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1)C1=CC=C2CCC=CC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 16, 16, 16, 74, 74, 74, 147, 201, 201, 201, 201, 201, 74, 74, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 74, 147, 147, 201, 201, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 809 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114200 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114200 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114200/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114200/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114200 Building REAL300020114201 mkdir: created directory `/scratch/stefan/7770410/working/building/REAL300020114201' /scratch/stefan/7770410/working/building/REAL300020114201 /scratch/stefan/7770410/working /scratch/stefan/7770410 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020114201 mkdir: created directory `0' /scratch/stefan/7770410/working/building/REAL300020114201/0 /scratch/stefan/7770410/working/building/REAL300020114201 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 0 (index: 2019) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/2019 `/scratch/stefan/7770410/working/3D/2019' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCNC(=O)C1CCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1) `REAL300020114201.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020114201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114201 none O=C(CCNC(=O)C1CCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 15, 21, 21, 21, 21, 58, 58, 58, 1, 1, 1, 1, 1, 7, 7, 7, 14, 23, 23, 23, 23, 23, 7, 7, 1, 15, 15, 21, 21, 21, 58, 58, 58, 58, 58, 58, 58, 3, 1, 1, 1, 1, 7, 14, 14, 23, 23, 1, 1] 201 rigid atoms, others: [43, 41, 42, 11, 12, 13, 14, 15, 50, 51, 27, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 289 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114201 none O=C(CCNC(=O)C1CCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 43, 54, 54, 54, 54, 121, 121, 121, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 43, 43, 54, 54, 54, 121, 121, 121, 121, 121, 121, 121, 11, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [45, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 458 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114201 none O=C(CCNC(=O)C1CCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 16, 10, 7, 7, 1, 7, 1, 1, 1, 1, 37, 39, 58, 58, 58, 121, 121, 121, 175, 201, 201, 201, 201, 201, 121, 121, 58, 16, 16, 10, 10, 7, 1, 1, 1, 1, 1, 1, 1, 39, 58, 58, 58, 58, 121, 175, 175, 201, 201, 58, 58] 201 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 39, 37] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 779 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114201 none O=C(CCNC(=O)C1CCC1)NC1CC(N2C=C(CCC3=N[N-]N=N3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 83, 92, 92, 92, 92, 201, 201, 201, 23, 23, 23, 7, 7, 7, 4, 2, 1, 1, 1, 1, 1, 1, 7, 7, 23, 83, 83, 92, 92, 92, 201, 201, 201, 201, 201, 201, 201, 27, 23, 23, 23, 23, 7, 4, 4, 2, 2, 23, 23] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 700 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114201 /scratch/stefan/7770410/working /scratch/stefan/7770410 mkdir: created directory `1' /scratch/stefan/7770410/working/building/REAL300020114201/1 /scratch/stefan/7770410/working/building/REAL300020114201 /scratch/stefan/7770410/working /scratch/stefan/7770410 Protomer 1 (index: 2020) Found valid previously generated 3D confromation in /scratch/stefan/7770410/working/3D/2020 `/scratch/stefan/7770410/working/3D/2020' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCNC(=O)C1CCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1) `REAL300020114201.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020114201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770410/working/building/REAL300020114201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114201 none O=C(CCNC(=O)C1CCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 15, 21, 21, 21, 21, 57, 57, 57, 1, 1, 1, 1, 1, 7, 7, 7, 14, 23, 23, 23, 23, 23, 7, 7, 1, 15, 15, 21, 21, 21, 57, 57, 57, 57, 57, 57, 57, 3, 1, 1, 1, 1, 7, 14, 14, 23, 23, 1, 1] 201 rigid atoms, others: [43, 41, 42, 11, 12, 13, 14, 15, 50, 51, 27, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 287 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114201 none O=C(CCNC(=O)C1CCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 43, 54, 54, 54, 54, 121, 121, 121, 7, 7, 7, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 1, 1, 7, 43, 43, 54, 54, 54, 121, 121, 121, 121, 121, 121, 121, 11, 7, 7, 7, 7, 1, 5, 5, 7, 7, 7, 7] 201 rigid atoms, others: [45, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 458 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114201 none O=C(CCNC(=O)C1CCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 16, 10, 7, 7, 1, 7, 1, 1, 1, 1, 37, 39, 57, 57, 57, 121, 121, 121, 175, 201, 201, 201, 201, 201, 121, 121, 57, 16, 16, 10, 10, 7, 1, 1, 1, 1, 1, 1, 1, 39, 57, 57, 57, 57, 121, 175, 175, 201, 201, 57, 57] 201 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 39, 37] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 780 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020114201 none O=C(CCNC(=O)C1CCC1)NC1CC(N2C=C(CCC3=NN=N[N-]3)N=N2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 83, 92, 92, 92, 92, 201, 201, 201, 24, 24, 24, 8, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 24, 83, 83, 92, 92, 92, 201, 201, 201, 201, 201, 201, 201, 28, 24, 24, 24, 24, 8, 4, 4, 2, 2, 24, 24] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 697 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770410/working/building/REAL300020114201 /scratch/stefan/7770410/working /scratch/stefan/7770410 Finished preparing REAL300020114201 Recording results /scratch/stefan/7770410/working /scratch/stefan/7770410 Appending to /scratch/stefan/7770410/finished/xaaaata.* 1: /scratch/stefan/7770410/working/building/REAL300020114201/1.* 0: /scratch/stefan/7770410/working/building/REAL300020114201/0.* Removing working files in /scratch/stefan/7770410/working/building/REAL300020114201 /scratch/stefan/7770410 Compressing combined databse files /scratch/stefan/7770410/finished/xaaaata.db2.gz /scratch/stefan/7770410/finished/xaaaata.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7770410/finished) ======================================================= Finalizing... removed `/scratch/stefan/7770410/working/3D/2021' removed directory: `/scratch/stefan/7770410/working/3D' `/scratch/stefan/7770410/working/protonate' -> `/scratch/stefan/7770410/archive' `/scratch/stefan/7770410/working/input-smiles.ism' -> `/scratch/stefan/7770410/archive/input-smiles.ism' rmdir: removing directory, `/scratch/stefan/7770410/working/building' rmdir: removing directory, `/scratch/stefan/7770410/working' ls: No match. ls: No match.